A new index for the assessment of hydromorphology in transitional and coastal waters around Ireland

Marine Pollution Bulletin 151 (2020) 110802

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A new index for the assessment of hydromorphology in transitional and coastal waters around Ireland

T

John Keogha, , Robert Wilkesa, Shane O'Boyleb ⁎

a b

Environmental Protection Agency, John Moore Road, Castlebar, Co Mayo, Ireland Environmental Protection Agency, Richview, Clonskeagh, Dublin 14, Ireland

ARTICLE INFO

ABSTRACT

Keywords: Hydromorphology Physical alteration Index development Transitional and coastal waters Water Framework Directive (WFD)

In assessing the overall status of individual water bodies the EU Water Framework Directive (WFD) requires member states to assess both ecological and chemical status. The ecological status of transitional and coastal (TraC) waters is based on the assessment of specific biological elements as well as supporting chemical, physicochemical and hydromorphological elements. Hydromorphology of TraC waters is one of the basic features of marine and coastal ecosystems controlling the presence of biota. Human induced hydromorphological alterations and pressures can damage the ecology and functioning of aquatic ecosystems. Thirteen metrics were developed and combined to form a hydromorphological index, the Hydromorphological Quality Index (HQI). The index categorises a water body into 5 classes. Semi-qualitative and quantitative criteria were used to assign a morphological classification directly related to that of the WFD, i.e., high, good, moderate, poor and bad. Thirtythree transitional and coastal water bodies were assessed using HQI.

1. Introduction The European Union Water Framework Directive (WFD 2000/60/ EC) commits member states to achieving ‘good ecological status’ for all water bodies and to ensure that there is no deterioration in status. In assessing the status of individual water bodies the WFD requires member states to assess both ecological and chemical status (European Commission, 2000). The ecological status of transitional and coastal waters bodies is based on the assessment of specific biological quality elements (phytoplankton, benthic invertebrates, macroalgae, angiosperms (seagrass and saltmarsh) and fish (transitional waters only)) as well as supporting chemical (specific pollutants), physico-chemical (e.g. temperature, salinity, nutrients) and hydromorphological elements (WFD2000/60/EC). Generally, there is a lack of quantitative data describing the relationship between hydromorphological conditions and ecological health of the biological elements. It is clear, that human induced hydromorphological pressures impacts on aquatic ecology (Environment Agency, 2009; EEA, 2012a; EEA, 2012b). It is recognized that different biological and morphological parameters may be more sensitive to certain hydrological or morphological processes than others and that the relative sensitivities will differ between different transitional and coastal environments (UKTAG, 2012). Hydromorphology is key to understanding functioning in ⁎

transitional and coastal waters and represents the link between sediments and suspended sediments, water movement and tidal balance, all of which influence the biota and are superimposed on the underlying geology/geomorphology of the system (Elliott and Whitfield, 2011). Structure includes sea bed geology, sediment features, morphology and water depth, whereas functioning includes hydrodynamics and sediment dynamics. Anthropogenic developments have caused substantial changes to the hydromorphology and biota of many water bodies throughout Europe (Chainho et al., 2008; Orlando-Bonaca et al., 2012; Pitacco et al., 2013; Recio et al., 2013; Gutperlet et al., 2015). In the latest assessment of European waters, the main significant pressure on surface waters (rivers, lakes and transitional and coastal waters) was hydromorphology (40%) closely followed by pollution from diffuse sources (38%) (EEA, 2018). The WFD requires member states to classify water bodies in terms of hydromorphology to support high ecological status (of fish, invertebrates, phytoplankton, macroalgae, seagrass and saltmarsh) and to put into place mitigation measures necessary to achieve at least ‘good’ status and prevent further deterioration of the status of water bodies (EEA, 2012a, 2012b). Hydromorphological pressures may also be relevant, particularly in relation to potential impacts on benthic invertebrates (Ysebaert et al., 2003; Borja et al., 2009; Josefson et al., 2009; Neto et al., 2010) and fish populations (Pérez-Ruzafa et al., 2006; Uriarte and Borja, 2009). The development of hydromorphology

Corresponding author. E-mail address: [email protected] (J. Keogh).

https://doi.org/10.1016/j.marpolbul.2019.110802 Received 19 September 2019; Received in revised form 22 November 2019; Accepted 3 December 2019 Available online 29 January 2020 0025-326X/ © 2019 Elsevier Ltd. All rights reserved.

Marine Pollution Bulletin 151 (2020) 110802

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Table 1 Hydromorphological characteristics of transitional and coastal waters as listed in this table of the guidance document (CEN, 2014) and the metrics for each generic feature. Assessment categories

No.

Generic features

Examples of attributes assessed

Metric

Morphology

1.

3.

Geology

Topography, bedforms, mouth width, intertidal area:subtidal area ratio; tidal volume; linear coastlines, beach types, shore armouring Presence of adjoining physical features and links within and between water bodies, and between transitional and coastal waters and wetlands; mouth width, presence of artificial structures (e.g. dams) Substrate type, bedform patterns

Metric 1a. Shoreline alteration

2.

Physiography/Depth/ Elevation Connectivity

4.

Biogenic structures

Presence of aquatic macrophytes and biogenic reefs

5.

Tidal regime, water level and current Wave regime Freshwater inputs and runoff Sediment dynamics

Current velocity and direction, water level variability, tidal range, tidal prism, presence of tidal wave/bore Exposure, wind speed and direction, fetch, wave height Residence time/flushing rate (transitional waters), retention time (enclosed bays), freshwater discharge Sediment supply, erosion/deposition/transport cycles

Stratification or degree of mixing

Salinity, turbidity, density, temperature

Hydrodynamic regime

6. 7. 8. 9.

Metric 2a. Presence or absence of barriers within and between water bodies Metric 3a. Bed disturbance Metric 3b. Change in habitat Metric 4a. Change in the spatial extent of Saltmarsh and Seagrass beds Metric 5a. Change in tidal regime Metric 6a. Changes in wave regime Metric 7a. Change in river flow Metric 7b. Change in residence time Metric 8a. Change in dominant fraction particle size Metric 8b. Change in turbidity Metric 9a. Change to stratification Metric 9b. Change in salinity

functioning of hydromorphological processes in transitional and coastal waters. More specifically, the assessment of hydromorphological condition will be needed in the process of designating heavily modified water bodies (HMWB). Under the WFD, where essential human activities and infrastructure may result in severe and permanent alteration to the character of a water body, that body of water can be designated as heavily modified. As such, the water body is not capable of achieving ‘good’ ecological status without significant adverse effects on use or the wider environment (see Borja et al., 2013). The Common Implementation Strategy (CIS) Guidance no. 4 (European Commission, 2000) outlines the steps involved in designation HMWBs, including “screening” water bodies and identifying “significant changes in hydromorphology” and “substantial changes in character due to physical alterations”. The process of designation would therefore be greatly aided by having a tool that could measure the degree of change caused by hydromorphological alterations and the impact of these alterations on the character of a water body. In this paper, we describe the development of a new hydromorphological condition assessment tool which is built around key features which characterise the hydromorphology of transitional and coastal waters (e.g. depth, connectivity, tidal regime, freshwater regime, residence time, sediment dynamics and water column mixing). This numerical index addresses the current lack of a hydromorphological classification tool for use in transitional and coastal waters in accordance with the WFD. It also represents a first step in developing a numerical index to measure the degree of hydromorphological alteration, a measurement which can be subsequently used to develop a better understanding of the relationship between these physical changes and their impact on biology. The HQI will also be a useful tool for managers to address hydromorphological pressures in transitional and coastal waters by providing a measure of the magnitude of the damage being caused by these pressures.

criteria and standards could support the introduction of a regulatory control system for hydromorphological alterations to surface waters and for classifying ecological status. de Jonge et al. (2012) presents an overview of a framework and component tools that can be combined to arrive at a set of suitable indicators to judge the systems condition or status in terms of health, resilience or carrying capacity. Suitable integral indicators matching the ecosystem approach and thus covering ecological as well as socio-economic aspects are required. There is also a need to determine how a pressure is changing the functioning and structure of the system. A review of research on hydromorphology with regard to the WFD carried out by Ioana-Toroimac (2018) found that the majority of research focused on rivers rather than lakes, transitional or coastal waters. Despite hydromorphological alterations being a threat to coastal water integrity the impact of these alterations has been explored to a much lesser degree (Orlando-Bonaca et al., 2012). Although work has been carried out on the response of biota to various levels of hydromorphological alteration, for example on rocky shores (OrlandoBonaca et al., 2012), benthic communities (Chainho et al., 2008) and estuarine vegetation (Recio et al., 2013). In Ireland the direct links between hydromorphological condition and ecological status has not been fully developed. In the absence of a fully developed condition assessment tool a risk-based tool known as the Transitional and Coastal Waters Morphological Impact Assessment System (TraC-MImAS) was developed. This desktop tool was designed to provide a risk-based regulatory decision-support tool to help regulators determine whether new projects likely to alter hydromorphological features could risk the ecological objectives of the WFD (UKTAG, 2013). It is limited, however, in its ability to fully characterise the hydromorphological structure and function in coastal and transitional waters (for example sea bed geology, sediment features, morphology and water depth, hydrodynamics and sediment dynamics). Feature categories to be assessed in hydromorphological characterisation and classification of transitional and coastal waters are outlined in the European guidance document (CEN, 2014). The assessment of hydromorphological condition needs to be informed by the collection of direct field observations that can be used to describe and measure change in key hydromorphological features. Furthermore, a measure of how these features might change in response to hydromorphological alterations is needed to assess the ability of these systems to support ecological functioning. This information will be vital in developing mitigation measures and as components in regulatory systems that will be required to sustainably manage activities that have the potential to damage the normal

2. Materials and methods Hydromorphological quality elements, for both transitional and coastal waters, are outlined in Annex V of the WFD (WFD, 2000/60/ EC). These include depth variation, sea bed morphology, structure of intertidal zone, freshwater flow, wave exposure and direction of dominant currents. The European guidance document (CEN, 2014) sets out nine feature categories for assessment in transitional and coastal waters and is collated in Table 1. The new index proposed here covers the nine generic categories (physiography/depth/elevation; 2

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Fig. 1. Water bodies assessed by HQI © Ordnance survey Ireland, All rights reserved, Licence number EN0059208

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connectivity; geology; biogenic structures; tidal regime, water level and current; wave regime; freshwater inputs and runoff; sediment dynamics; stratification or degree of mixing see below) identified in the guidance and uses a mixture of field-based and GIS observations to populate the metrics used to measure each of these generic features. Thirty-three water bodies were examined (see Fig. 1) covering a range of water body types; TW2, CW2, CW5 and CW8. The 13 selected metrics cover all the 9 feature categories listed in the guidance document. For the majority of generic features categories one metric was selected. In the case of geology, freshwater inputs and runoff, sediment dynamics and stratification or degree of mixing two metrics were selected for each feature category. The selection of the second metric in these feature categories reflects the data (e.g. salinity, particle size, turbidity, saltmarsh and seagrass beds) collected on a regular basis for the Irish WFD national monitoring programme. No testing was carried out on the individual performance of each metric. While some of the metrics used in HQI use some of the same information assessed by TraC-MImAS (shoreline alteration, presence of barriers, bed disturbance, change in habitat, wave regime), it also incorporates metrics based on in-situ data collected during ongoing monitoring programmes (change in extent of saltmarsh and seagrass, tidal regime, change in river flow, change in residence time, change in dominant sediment fraction, change in turbidity, change to stratification, change to salinity) such as the national WFD programme. A description of each metric and the rationale for its inclusion in the index is given below. The ability of a metric to measure change in a feature, and the implications of that change on biological communities and the ecology of transitional and coastal waters is also outlined. The majority of morphology based metrics (shoreline alteration, presence or absence of barriers, change in habitat) change is assessed against ‘historic times’ (> 50 years). In the other metrics change was determined by comparing 2014–2016 data to the 2007–2009 data. The metrics for each of the 9 generic features are summarised in Table 1 and the scoring systems for each metric is in Table 2.

hydromorphology can only be applied as a check for high status waters. However, an assessment method is needed to assess the extent of the impact in water bodies being damaged by hydromorphological pressures. There is also a need for a system to describe the magnitude and gradient of pressures. This is needed to assess the effects on hydromorphological and biological processes and to better prioritise measures. In this case, as proposed here, a multiclass assessment system representing the gradient of pressures and impacts is required. The 5 classes proposed here aligns with the concept and normative definition already used in the WFD. Thirteen Metrics, covering all the 9 generic feature categories were selected (see Table 1). Metrics evaluate the degree of alteration (due to anthropogenic activity) away from the ‘reference’ condition. In the majority of metrics (4a, 5a, 7a, 7b, 8a, 8b, 9a and 9b) available data was used to assign a score to the metric in question. In the remaining metrics (1a, 2a, 3a, 3b and 6a) condition categories (High, Good, Moderate, Poor and Bad) follow those used in the River Hydromorphology Assessment scheme (NIEA, 2009). In all cases the baseline used refers to the near-natural condition. Two primary data sources were used: GIS datasets of morphological alterations and WFD monitoring data. In this project a 50 m buffer zone was added as an extension to the WFD water body boundary area. The buffered water body boundary approach was used to better capture particular morphological alterations. Morphological alterations such as shoreline reinforcement or embankments, and habitats such as sand dunes, are generally located landward, with some or all of such features often falling outside of the WFD water body boundary. Certain extents of morphological alterations and habitats would not be captured to an appropriately representative extent by the WFD water body boundary area. An example of the spatial data layers used in the calculation of HQI in Cork Harbour is shown in Fig. 2. Metric 1a. Shoreline alteration Shoreline areas support a great diversity of marine life and habitats (e.g. sandy shores, rocky shores and saltmarsh) and as such the alteration of the shoreline can have profound effects on the ecology of transitional and coastal waters. Many of these impacts are indirect and the effects are wide-ranging and long-lasting. Estuarine mud and sand flats play an important role as nursery and feeding areas for marine fish (Elliott and Dewailly, 1995), with mudflats and saltmarsh habitats also providing important feeding grounds for fish species (Environment Agency, 2009). As well as reducing the extent of marshes, shoreline alteration in estuaries has resulted in the more rapid passage of the flood tide up the estuary, increasing erosional pressures on remaining marshes, which are unable, in some cases, to retreat landward as they are backed by sea defences (Environment Agency, 2009). Data for this metric was obtained from GIS layers. Sections of shoreline were mapped with lengths of hard engineering reinforcement, soft engineering reinforcement and flood defence embankments. Total length of altered coastline was determined. Alteration was then expressed as a percentage of the total shoreline in the water body. See Table 2 for the scoring of this metric. Metric scorings follows the RHAT (NIEA, 2009) assessment scheme.

Metric boundary conditions Boundaries were set to align with the normative definitions of the degree of deviation from reference/undisturbed conditions used in the WFD. With each boundary representing the spectrum of deviation from no change to slight, moderate, major and severe. Boundary values were developed based on existing methods, expert judgement and empirical evidence. For example, for metrics 1a, 2a, 3a, 3b, boundary values used the same values as applied in the existing River Hydromorphology Assessment Technique (RHAT) scheme (NIEA, 2009). These boundaries are based on the percentage (%) deviation (for example 5%, 15% etc.) from reference condition. For other metrics, such as metric 4a (change in the extent of saltmarsh and seagrass beds), boundaries were based on intercalibrated WFD assessment tools and were selected based on the ecological response to pressure (Wilkes et al., 2017; Penk et al., 2018). These boundaries may change after further development, testing and validation. The degree of change represented by the boundaries for the turbidity, stratification and residence time metrics were based on our current understanding of how changes in each of these metrics would impact on ecological functioning. (see Jones and Gowen, 1990; Valiela et al., 1997; Painting et al., 2007; O'Boyle et al., 2015; Ní Longphuirt et al., 2016).

Metric 2a. Presence or absence of barriers within and between water bodies

Metric formulation and data sources

Barriers present a major alteration to the hydromorphology of transitional and coastal waters. The existence of an estuarine barrier (e.g. seawalls, piers, bridges, viaducts) may cause changes in current patterns or sedimentation. The restriction of the tidal wave, both entering and leaving the estuary, will change the tidal regime by reducing the tidal amplitude (McLusky and Elliott, 2004). Changes in wave exposure and current speed can modify the composition of saltmarsh and seagrass beds (Recio et al., 2013). Barriers can disrupt migration of fish

Thirteen metrics were combined to form a single hydromorphological metric, the Hydromorphology Quality Index (HQI). The HQI classifies hydromorphology based on the departure from naturalness and assigns a hydromorphological classification directly related to that of the WFD: High, Good, Moderate, Poor and Bad based on semiqualitative and quantitative criteria. The WFD states that 4

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Table 2 Metrics used and scoring system for the determination of the Hydromorphological Quality Index. Morphology 1.Physiography/Depth/Elevation

2. Connectivity

3. Geology

4. Biogenic structures

Metric 1a: Shoreline alteration Shoreline is in natural condition. < 5% of shoreline altered. Slight alterations on the shoreline. 5% to 15% of the shoreline altered. Moderate shoreline alteration. 15% to 35% altered Major shoreline alteration. 35% to 75% altered Severe alteration of the seashore. > 75% altered. Metric 2a: Presence or absence of barriers There are no barriers to impede water movement. < 5% of the width of the water body blocked. Presence of minor artificial structures such as groynes, bridges and jetties. 5% to 15% of the water body width blocked. Water movements are impeded by features that extend across the entire water body but water can pass through, e.g. bridge.15% to 35% of water body width. Water movement is impeded to a major extent. 35% to 75% of water body width blocked. Water movement is severely impeded. > 75% of water body width blocked. Metric 3a: Bed disturbance Relative bed disturbance based on pressures and activities. (% of area affected) Little or no bed disturbance. < 5% bed disturbance. Slight bed disturbance. 5% to 15% disturbance. Moderate bed disturbance. 15% to 35% disturbance. Major bed disturbance. 35% to 75% disturbance. Severe bed disturbance. > 75% bed disturbance. Metric 3b: Change in habitat Little or no habitat loss. < 5% Slight habitat loss. 5 to 15% Moderate habitat loss. 15 to 35% Major habitat loss. 35 to 75% Severe habitat alterations. > 75% Metric 4a: Change in the spatial extent of Saltmarsh and Seagrass beds Little or no habitat loss. < 5% Slight habitat loss 5 to 15% Moderate habitat loss. 15 to 35% Major habitat loss. 35 to 75% Severe habitat alterations. > 75%

Score 0 1 2 3 4 Score 0 1 2 3 4 Score 0 1 2 3 4 Score 0 1 2 3 4 Score 0 1 2 3 4

Hydrodynamic regime 5. Tidal regime, water level and current

6. Wave Regime

7. Freshwater runoff and residence time

8. Sediment dynamics

9. Stratification or degree of mixing.

Metric 5a: Change in tidal regime No change Slight change. < 50% within a tidal category Moderate Change > 50% within a tidal category Major change. Tidal regime altered by one category. Microtidal to mesotidal, mesotidal to macrotidal etc. Severe change. Tidal regime changed by two categories. Microtidal to macrotidal, macrotidal to microtidal. Metric 6a: Change in wave regime Area influenced by structures/area of water body Minor change. < 5% of the water body area influenced by structures Slight change. 5% to 15% of the water body area influenced by structures Moderate change. 15% to 35% of the water body area influenced by structures. Major change. 35% to 75% of the water body area influenced by structures. Severe change. > 75% of the water body area influenced by structures. Metric 7a: Change in river flow Minor change in freshwater input (< 5% change in LTAA) Slight change in freshwater input (5 to 15% change in LTAA) Moderate change in freshwater input (15% 35% change in LTAA) Major change (> 35 change in LTAA) 7b. Change in Residence Time No change to residence time Slight change to residence time. < 50% within a residence time category Moderate change to residence time. > 50% within a residence time category Major change to residence time (days to weeks, weeks to months etc.) Severe change to residence time (days to months, months to days) Metric 8a: Change in dominant fraction particle size Little or no change in sediment composition (< 5%) Slight change in the dominant sediment fraction composition (5–15%) Moderate change in dominant sediment fraction composition (15–35%) Major change in dominant sediment fraction composition (35–75%) Severe change in dominant sediment fraction composition (> 75%) Metric 8b: Change in Turbidity No change to turbidity Slight change to turbidity. Change of 1 class Moderate change to turbidity (change of 2 class) Major change (change in 3 classes) Severe change in turbidity (change in > 3 classes) Metric 9a: Change to stratification No change to stratification

Score 0 1 2 3 4 Score 0 1 2 3 4 Score 0 1 2 4 Score 0 1 2 3 4 Score 0 1 2 4 6 Score 0 1 2 4 6 Score 0

(continued on next page) 5

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Table 2 (continued) Hydrodynamic regime Slight change in stratification. > 50% change within stratification category. Moderate change in stratification. (Stratified to partial stratified. Partially stratified to mixed. Mixed to partially stratified. Partially stratified to mixed.) Major change in tidal regime. Changes from mixed to stratified and vice versa. Metric 9b: Change in salinity No change in salinity Slight change in salinity. 1 salinity band change (e.g. freshwater to oligohaline, polyhaline to euhaline etc.) Moderate change in salinity. 2 salinity band change (e.g. freshwater to mesohaline) Major change in salinity. 3 salinity band change (e.g. freshwater to polyhaline) Severe change in salinity. 4 salinity band change (e.g. freshwater to euhaline)

1 2 4 Score 0 1 2 3 4

and opportunities for recruitment in to the estuarine system. Barriers can also cause salinity fluctuations detrimental to the survival of many species (Pease, 1999). A GIS data layer was used to identify the presence or absence of barriers (impoundments, bridges and piers). The percentage width of a barrier across a water body was determined. See Table 2 for the scoring of this metric. Metric scoring follows the RHAT (NIEA, 2009) assessment scheme.

area was expressed as a percentage of the total water body area. Physical disturbance shall be understood to mean: a change to the seabed from which it can recover if the activity causing the disturbance pressure ceases (European Commission, 2017). See Table 2 for the scoring of this metric. Metric scoring follows the RHAT (NIEA, 2009) assessment scheme.

Metric 3a. Bed disturbance

Loss of habitat (through land claim and building infrastructure) changes the shape, hydrography and sediment patterns of an estuary as well as removing feeding (e.g. mudflats) and refugia (e.g. saltmarsh) areas (Environment Agency, 2009). In the adjacent area, the effects can range from shifts in the aquatic plant composition (Egertson et al., 2004) to alterations in the benthic communities (Recio et al., 2013). A GIS data layer (Land Claims) was used to determine the area of a water body habitat lost to anthropogenic activity. This area was expressed as a percentage of the total water body area Loss was considered as a permanent change which has lasted or is expected to last for a period of 12 years (two reporting cycles under the Marine Strategy Framework Directive) or more (European Commission, 2017). See Table 2 for the scoring of this metric. Metric scoring follows the RHAT

Metric 3b. Change in habitat

Activities such as fishing and dredging can cause disturbances of the seabed. Fishing activity can modify the substrate and disturb benthic communities. Turbidity changes from dredging or dumping of dredging spoils effects the light regime (Karel, 1999). Increased localised turbidity is a limiting factor for phytoplankton production in estuarine ecosystems, which may be limited by light availability for photosynthesis (Environment Agency, 2009). Loss of sediment through dredging can affect the food and space resource (Elliott and Hemingway, 2002). GIS data from licensed areas was used to determine the area affected by dredging, aquaculture, fishing activity and pipelines. The affected

Fig. 2. Morphological alteration map of Cork Harbour. 6

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(NIEA, 2009) assessment scheme.

at the expense of saltmarsh with marsh recovery in inter-storm periods (Environment Agency, 2009). Based on work developed in the TraC-MImAS assessment, changes in wave regime were measured using piled structure as a proxy for change. Offshore structures, such as detached breakwaters, surfing reefs, wind and wave turbines and offshore platforms, all have the potential to affect the wave regime over part of a water body. Bridges and piled structures in the subtidal zone are also considered. Area of piled structure was determined from a ‘Piled Structures’ GIS data layer. This area was multiplied by 10 to determine the area influenced by piled structures (Environment Agency, 2005). See Table 2 for the scoring of this metric.

Metric 4a. Change in the spatial extent of Saltmarsh and Seagrass beds Saltmarshes and seagrass provide rare and unique habitats and are important for fish and wildlife and vital feeding grounds for a wide variety of migratory bird species. Saltmarshes have a significant positive effect on wave attenuation and shoreline stabilisation (Shepard et al., 2011). In the context of climate change, saltmarshes are recognized as being very important in sequestering carbon (Chmura et al., 2003). Dense seagrass meadows significantly attenuate water flow (Koch and Gust, 1999; Peterson et al., 2004) and provide shelter and food to a diverse community of animals. They are also used as indicators of ecological status (Wilkes et al., 2017). Saltmarshes provide a broad range of high-value services to both terrestrial and aquatic ecosystems (de Groot et al., 2012). These include dissipation of wave energy, sediment trapping, carbon storage, nutrient cycling and trophic subsidies to aquatic food webs (reviewed in Weis et al., 2016). Saltmarsh (Devaney and Perrin, 2015) and seagrass (Wilkes et al., 2017) are two of the specified biological quality elements used in assessing ecological status for the WFD and their assessment include a measure of the percentage change in area. For each biological community the changes in spatial extent was assessed and where both elements occur in the same water body, the highest score was used to determine the metric score. The distribution of these two biological quality elements is restricted around the Irish coast, therefore information is not available for all water bodies. Current area occupied by seagrass/saltmarsh is compared to baseline area. See Table 2 for the scoring of this metric. Change is defined as a difference in state between measurement periods.

Metric 7a. Change in river flow Change in freshwater input (e.g. through abstraction) will influence the supply (loading) and concentrations of nutrients, the location of the freshwater–seawater interface (which changes phytoplankton community structure), the residence time (which impacts on nutrient supply in estuarine and coastal zone) and the mixing of the estuary (affecting phytoplankton growth). All these impacts may also have a knock-on effect on phytoplankton production in estuarine and coastal waters (Environment Agency, 2009). Long Term Average Flow (LTAA) was used to determine changes (increases and decreases) in freshwater input into transitional and coastal water bodies. River flow data is mainly applicable to transitional waters and coastal waters with a single discharge into the water body. Data was obtained from the EPA and OPW (Hydronet.ie) and OSPAR (see Riverine Inputs and Direct Discharges (RID) online). The percentage change in LTAA was determined by comparing data from 2012 to the 10-year average flow from 2002. See Table 2 for the scoring of this metric.

Metric 5a. Change in tidal regime

Metric 7b. Change in residence time

Tidal range and frequency has been shown to have a profound effect on the hydrology, morphology and habitats of transitional and coastal waters (Kirwan and Guntenspergen, 2010). Tidal regime can influence hydrology through its influence on water movements (current velocity), residence time and the degree of mixing between freshwater and seawater. The tidal regime will also effect tidal bed stress, erosion and deposition patterns and hence the composition of the substratum. These hydrological and morphological factors can in turn effect the lateral and vertical distribution of marine organisms on the shore; the dispersal of larvae, the composition of intertidal organisms and the accumulation of macroalgae and phytoplankton blooms under different tidal bed stress and residence time scenarios (Aldridge and Trimmer, 2009; Levin, 2006; Ní Longhphuirt et al., 2016). The tidal regime was classified according to three categories, microtidal (< 2 m), mesotidal (2 to 4 m) and macrotidal (> 4 m) (see Davies, 1964). Admiralty data was used to determine if there was a change in the tidal regime. See Table 2 for the scoring of this metric.

Residence time has an important role to play in controlling phytoplankton biomass in estuaries and changes in this factor could have important implications for phytoplankton production, particularly if residence times were to increase. Short residence times in nutrientenriched estuaries may favour the development of bottom-growing macroalgal blooms. In estuaries with longer residence times, phytoplankton growth in the water column can attenuate light reaching the bottom restricting the growth of attached macroalgae. However, in estuaries with short residence times, phytoplankton growth is likely to be inhibited by physical retention time, and in such cases, sufficient light may reach the bottom to support the growth of macroalgal blooms (O'Boyle et al., 2015). Two methods are used to estimate residence time depending on the hydromorphological characteristics of the water body (see O'Boyle et al., 2015). For the upper sections, and some of the mid-section estuaries, a simple freshwater replacement time for calculating the mean freshwater residence time was used:

Metric 6a. Change in wave regime

fw =

Changes in wave regime determines the degree of exposure experienced by shoreline communities and can alter the composition and biomass of these communities (e.g. Viana et al., 2015). For example, wave regime can control and determine the stability of macroalgal communities. Wave action causes physical damage to macroalgae and this is magnified in areas where algae are immersed and prone to desiccation. Intertidal mudflats frequently show annual and inter-annual variations in surface elevation, reflecting phases of surface erosion and accretion. However, saltmarshes are characterised by more stable surfaces that build up incrementally. The dynamic boundary between the two habitats is related to wave climate as wave induced stresses determine the survival of saltmarsh seedlings; storms may extend mudflat

Vfw Qfw

where, Vfw is the volume of freshwater in the estuary and Qfw is the input rate of freshwater. This ratio gives the time required for the inflowing freshwater to replace the freshwater already in the estuary. The volume of freshwater in the estuary is calculated as the amount of freshwater that must be mixed with seawater having salinity (Ss) equal to that entering at the seaward boundary to yield a volume Ve equal to that of the estuary, with salinity equal to the mean salinity of the estuary (Se). Vfw may be calculated as:

Vfw = 1 7

Se Ve Ss

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Table 3 Turbidity categories used. Turbidity category Very high High Medium Intermediate Low Very low

Secchi depth (m)

Suspended particulate matter range (mg/l)

Kd (m−1)

Photic depth (m) (approximation)

Turbidity (NTU) (approximation)

< 0.1 < 0.5 <2 <4 >4 > 10

> 250 > 50 > 10 >5 <5 <1

> 17 > 3.5 > 0.85 > 0.43 < 0.43 < 0.15

< 0.5 < 1.0 < 5.0 < 10.0 > 10.0 > 30.0

> 100 > 25 >5 >2 <2 0.5

For the lower sections and coastal bays, and some of the mid sections, a tidal prism model, derived from model simulations of Irish coastal water bodies (see Hartnett et al., 2011), can be calculated as:

Tr =

8.65 TPR

2.45 × B0 + 0.59 × L

where a high level of suspended particulate material may severely restrict the availability of light. The amount of photosynthetically active radiation in natural waters is of fundamental importance in determining the growth of aquatic plants. Primary production by phytoplankton is a light dependent process that provides the energy to drive the plankton and microbial food web that typically takes place down to depths to which about 1% of surface light penetrates (i.e., the euphotic zone) (Devlin et al., 2008). In seagrass survival and growth is dependent on a wide variety of factors, with light availability identified as one of the main controlling factors (Environment Agency, 2009). This metric is based on the degree of change in the concentration of suspended particulate matter in the water column. While turbidity is mentioned in ‘stratification or degree of mixing’ (Generic feature no. 9) in the Guidance Document it was deemed that using turbidity to assess ‘sediment dynamics’ (Generic feature no. 8) was a more appropriate metric for assessing changes in sediment dynamics. Turbidity is routinely measured in the WFD monitoring programme using a Secchi disk to determine the Secchi depth. Photic depth (Zp), the depth where the irradiance is 1% of that immediately below the water surface, is calculated using the light attenuation (Kd) coefficient (Zp = 4.61/Kd). Kd can be estimated from Secchi depth (m) measurements (Kd = 1.7/ Secchi depth). The potential for phytoplankton growth based on light availability is estimated by comparing the ratio of mixing depth to photic depth. When this ratio is > 5, phytoplankton growth is considered to be light limited, i.e. respiratory loss is likely to exceed primary productivity (Cole and Cloern, 1984; Cloern, 1987). Mixing depth is taken as the median water column depth except for those areas where a halocline or thermocline was present, as defined by an increase in salinity with depth > 0.5 salinity units m-1 or a surface to bottom temperature difference > 4 °C. In such cases, the depth of the surface mixed layer is taken as half the water column depth (O'Boyle et al., 2015). Water bodies were classified according to their turbidity (see Table 3 below). 2014–2016 data was compared to 2007–2009 data to assess change. The summer median Secchi depth was used to determine the turbidity of a water body. See Table 2 for the scoring of this metric.

5.05

where, TPR is the tidal prism ratio, B0 is the width of the mouth of the estuary and L is the length of the estuary along the longitudinal axis. The TPR is calculated as:

TPR =

TP

where V is the volume of the estuary and TP is the tidal prism volume or the volume of water between low water and high water. This metric looks at changes in the residence time in a water body. Three residence time categories are used: days, weeks and months. See Table 2 for the scoring of this metric. Metric 8a. Change in dominant fraction particle size (sediment characteristics) The benthos is intimately linked to changes to the sedimentology and thus the hydrography, and in turn it has the potential to modify the sediment physical and chemical characteristics (see Phillips et al., 2014). Substratum features are the result of hydro-geomorphological processes including the hydrological influences on the underlying geology. Any activity on the seabed can have an adverse effect on macrobenthic community (Orlando-Bonaca et al., 2012). The creation of areas with low hydrodynamic energy will lead to the accumulation of fine sediments, organic matter and contaminants. The resulting fine materials prevent water movement through the sediments, reducing oxygen and the breakdown of organic matter and in turn adversely affects the benthic infauna (Environment Agency, 2009). Other pressures that affect substratum integrity and thus the benthos include fishing activities, coastal engineering projects and physical disturbance. For example, trawling, mechanical harvesting, mechanical dredging and aggregate extraction have a major impact on the coastal and transitional waters benthic communities (Environment Agency, 2009). Particle size analysis (PSA) is undertaken as part of the WFD benthic monitoring programme. Data being gathered as part of the national WFD programme and is patchy. Data is collected on a 6-year cycle, therefore we do not have adequate data to look at change many waterbodies. Particle size is determined using the Wentworth scale (Wentworth, 1922). This metric looks at the dominant sediment fraction of samples. PSA data for benthic survey in a water body is combined. The mean percentage of each sediment fraction was calculated and the dominant fraction determined. This metric assesses the change in the dominant fraction mode. Available 2014–2016 data was compared to 2009–2012 data to assess change. See Table 2 for the scoring of this metric.

Metric 9a. Change to stratification The vertical mixing state (stratified or otherwise) of the receiving body and the residence/flushing time of the freshwater and its nutrients in the system determine the sensitivity of systems to developing symptoms of eutrophication (de Jonge and Elliott, 2001). In a stratified estuary, the freshwater–seawater interface is very efficient in collecting living and detrital particles from the highly productive brackish water layer, thus playing an important role in determining the distribution and fate of organic matter in the estuary. In a well-mixed estuary, river discharges and tidal mixing result in a strong estuarine circulation and an intense exchange between the estuary and coastal waters, thus distributing the organic matter throughout both systems (Environment Agency, 2009). Water body stratification was categorised into three classes; mixed, partially stratified, stratified. The Potential Energy Anomaly (φ) was used to determine the degree of mixing in each of the water bodies (Simpson et al., 1990).

Metric 8b. Change in turbidity For aquatic plants, the sub-surface light climate has a major influence on growth particularly in inshore and nearshore environments 8

9

0.73

0.9

0.98 0.71

0.81 0.83 1.00 0.88 0.80 0.91 0.63

0.91

0.82 0.86 0.85

Good

High Moderate

Moderate Moderate High Good Moderate Good Poor

Good

Moderate Good Good

0.88 0.80 0.76

Good Moderate Moderate

Moderate

0.92

Good

0.91 0.71 0.79

0.89

Good

Good Moderate Moderate

0.81 0.87 0.85 0.95 0.93

Moderate Good Good High Good

0.67

0.96

High

Moderate

0.91 0.93 0.94

Good Good Good

Corrib Estuary Outer Galway Bay Inner Galway Bay North Inner Galway Bay South Lee (K) Estuary Inner Tralee Bay Outer Tralee Bay Waterford Harbour Barrow Suir Nore Estuary New Ross Port (HMWB) Lower Suir Estuary (HMWB) Middle Suir Estuary Tolka Estuary Liffey Estuary Lower (HMWB) Liffey Estuary Upper Dublin Bay Cork Harbour Lough Mahon (HMWB) Lee (Cork) Estuary Lower Inner Kenmare River Killala Bay Rosslare Harbour (HMWB) Dungarvan Harbour Colligan Estuary Donegal Bay South Gweebarra Estuary Garavoge Estuary Courtmacsherry Bay Boyne Estuary (HMWB) Mouth of the Shannon Upper Shannon Lower Shannon Fergus Estuary

HQI score

HQI

Water Body

3 1 2

1

2 2 0 0 2 0 3

0 4

0

4

3 3 2

4

2 4 4

1

1

1 1 0 0 1

0

2 0 0

1a: Shoreline alteration

0 0 0

0

0 1 0 2 1 1 3

0 1

1

1

0 1 1

2

0 1 1

1

2

1 0 0 0 0

0

2 0 0

2a: Presence or absence of barriers

1 3 0

2

3 1 0 0 3 2 3

0 4

0

3

0 2 1

0

1 0 3

1

2

4 4 4 2 2

1

1 2 2

3a: Bed disturbance

0 0 0

0

0 0 0 0 0 0 3

0 0

0

1

0 0 0

4

0 1 1

0

0

0 0 0 0 0

0

0 0 0

3b: Change in habitat

4 3 3

–

– 2 – 3 3 – 1

1 –

–

–

0 – –

–

– – –

0

–

– 0 – – –

–

0 – 0

4a: Change in the extent of Saltmarsh and Seagrass beds

0 0 0

0

0 0 0 0 0 0 0

0 0

0

0

0 0 0

0

0 1 0

0

0

0 0 0 0 0

0

0 0 0

5a: Change in tidal regime

Table 4 Hydromorphology Quality Index (HQI) score and classification and individual HQI metric scores for each water body.

0 0 0

0

0 0 0 0 0 0 0

0 0

0

0

0 0 0

3

0 2 0

1

0

0 0 0 0 0

0

0 0 0

6a: Changes in wave regime

0 0 0

0

0 – – – – – –

0 0

0

1

1 1 1

0

0 0 0

0

0

– – – 0 0

–

0 – 0

7a: Change in river flow

0 0 0

0

0 0 – 0 0 0 0

0 0

–

0

0 0 0

0

0 0 0

0

0

0 0 – 0 0

0

0 0 0

7b: Change in residence time

0 – 1

–

– – – – – – –

– –

–

–

– – –

–

– – –

–

–

– – – – –

–

– – –

8a: Change in dominant fraction particle size

1 0 0

–

1 0 – 0 0 – 0

0 –

2

0

0 0 0

0

– 0 0

0

0

1 0 – 0 0

–

0 – 0

8b: Change in turbidity

1 0 2

–

0 – – 0 0 – 4

0 –

0

0

0 1 0

0

0 0 1

0

0

0 0 0 0 0

–

0 – 0

9a: Change to stratification

0 0 0

–

0 1 – 0 0 – 0

0 –

1

0

0 0 0

1

– 1 1

0

0

1 0 – 0 0

–

0 – 0

9b: Change in salinity

J. Keogh, et al.

Marine Pollution Bulletin 151 (2020) 110802

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J. Keogh, et al.

( )=

1 h

0 h

(

) g . zdz

:

=

1 h

0 h

High (> 0.95), Good (> 0.85–0.95), Moderate ( > 0.65–0.85), Poor (> 0.25

dz

–0.65), Bad ( <0.25).

where h is the water column depth and ρ the sea water density (kg m−3) at depth z (m) and g is the acceleration due to gravity (m s−2). The value of (φ) (J m−3) is the energy required per unit volume to bring about complete vertical mixing and is thus directly proportional to the strength of stratification. Values of (φ) < 10 J·m−3 indicate that the water column is well mixed (φ) = 10–30 J·m−3 indicate that the water column is partially stratified (φ) > 30 J·m−3 indicate that the water column is well stratified Mean surface and bottom water density was determined using summer mean surface and bottom temperature and summer mean surface and bottom salinity for each water body. Mean bottom sample depth was used to determine h. Data from the EPA's WFD monitoring programme 2014–2016 data compared to the 2007–2009 data. See Table 2 for the scoring of this metric.

3. Results Thirty-three transitional and coastal water bodies (see Fig. 2) were assessed using the HQI (Table 4). The HQI scores ranged from 1.0 (Donegal Bay Southern) indicating a high classification to 0.63 (Boyne Estuary) indicating a poor classification. No water bodies were assessed as bad. Four water bodies were classed as high, 16 classed as good and 12 classed as moderate and one classed as poor. Donegal Bay Southern is a coastal water body with an area of 573.091 km2. This water body is predominantly subtidal with only 2% of the total area of the water body comprised of intertidal area. Donegal Bay Southern has a typology of ‘Moderately to exposed coastal-sedimentary’ (CW2) (Sniffer/Royal Haskoning, 2012a). The HQI score for this water body is as expected as, apart from fishing, there is very little hydromorphological alteration in Donegal Bay. The Boyne Estuary is a transitional water body with an area of 3.164 km2 comprising almost entirely of subtidal area. The Boyne Estuary, is an urban estuary, running through the urban area of Drogheda, a medium sized Irish town. There has been significant amount of historic hydromorphological alteration (canalised training walls) to this water body such as The Drogheda Port Company which operates two facilities for the loading/discharging of cargoes, the inner north quays port and a deep-water port facility. The low HQI score (0.63) for the Boyne Estuary is as expected due to the extensive hydromorphological alteration in this water body. Seven of the water bodies assessed are designated as Heavily Modified Water Bodies (e.g. Liffey Estuary Lower, Rosslare Harbour, New Ross Port, Lower Suir Estuary, Lee (Cork) Estuary Lower, Lough Mahon and Cork Harbour). Two HMWBs water bodies (New Ross Port and Lower Suir Estuary) had an index score indicating good. As such, further investigation is needed to examine the potential effect on biology and the appropriateness of heavily modified water body designation in these two water bodies. The other five HMWBs (Liffey Estuary Lower, Rosslare Harbour, Lee (Cork) Estuary Lower, Lough Mahon and Cork Harbour) had a moderate score which is more consistent with their designation as a HMWB. The number of metrics used for the calculation of HQI in each water body varied depending on available data. In general, there was more data available from water bodies close to urban areas particular on the east and south-east coasts. Mean number of metrics used for analysis of each water body was 10.4. Six metrics were used in the assessment of HQI in Donegal Bay South while all 13 metrics were used in the assessment of Corrib Estuary, Fergus Estuary and Upper Shannon. In the majority of cases the final HQI score is driven by the morphological metrics in particular Shoreline Alteration (1a) Barriers (2a) and Bed Disturbance (3a). Examples of waterbodies where these three metrics drive the HQI are the Corrib Estuary (good), Lee (Kerry) Estuary (moderate), New Ross Port (good), Liffey Estuary Lower (good), Liffey Estuary Upper (moderate), Cork Harbour (moderate), Lough Mahon (moderate), Lee (Cork) Estuary Lower (moderate), Rosslare Harbour (moderate), Colligan Estuary (moderate) and Garavoge Estuary (moderate) and Boyne Estuary (poor). Corrib Estuary, New Ross Port, and Liffey Estuary Lower were classed as Good. All the other water bodies were classed as moderate. Where waterbodies were classed as High, (Inner Galway Bay, Killala Bay and Donegal Bay Southern) these three metric played a slight (Metric 3a. Bed disturbance in Inner Galway Bay South) or no role in the determination of HQI. In total, twelve water bodies were classed as moderate. Shoreline alteration (1a), Bed Disturbance (3a), Change in habitat (3b), Presence or absence of Barriers (2a) and Change in the spatial extent of Saltmarsh and Seagrass (4a) were the main metrics determining a moderate classification in these water bodies. Shoreline alteration (1a) and Bed Disturbance (3a) play an important role in the moderate classification of water bodies. Twelve water bodies were classified as moderate

Metric 9b. Change in salinity Salinity, due to its influence on the physiology of marine organisms is one of the main factors controlling the distribution and composition of estuarine communities (Gunter, 1961; Ysebaert et al., 2003). Fluctuations in salinity due to changes in freshwater inputs can also affect the physical structure of estuaries and nearshore coastal waters and this in turn can impact on estuarine and marine fauna, flora and habitats (Gillanders and Kingsford, 2002; Ogden and Davis, 1994). For example, the distribution and composition of phytoplankton species (Kies, 1997) and benthic faunal communities (Ysebaert et al., 2003) has been observed to change along the salinity gradient of an estuary from freshwater to coastal waters. Freshwater phytoplankton die once they reach the freshwater-seawater interface and marine phytoplankton are less tolerant of brackish conditions; hence the estuarine phytoplankton community composition will be dominated by fewer species that can tolerant changes in salinity. Similarly, freshwater phytoplankton die once they reach the freshwater-seawater interface; hence the estuarine phytoplankton community composition will be dominated by euryhaline species. Data from the EPA's WFD monitoring programme was used to determine changes in salinity in the water bodies. Median summer salinity across the water column of the water body was used to determine the salinity band category of a water body. Transitional and coastal water bodies were classified according to the following salinity bands: freshwater, < 0.5; oligohaline, 0.5 to < 5.0; mesohaline, 5.0 to < 17.5; polyhaline, 17.5 to < 30; euhaline, > 30. While these categories differ slightly from the WFD they are used here to reflect Irish conditions. Data from the period 2014–2016 was compared to 2007–2009. Changes in salinity category over this period were determined. See Table 2 for the scoring of this metric. Hydromorphological Quality Index calculation Each metric was assessed by calculating the amount of deviation from the baseline condition. For each water body, the score (deviation) from all the metrics are summed. The sum of all the recorded deviations gives the Total Deviation (Stotal). The maximum possible deviation for each water body gives the Maximum Deviation (Smax). A Hydromorphological Alteration Index (HAI) is calculated by:

HAI = Stotal /Smax The HQI is calculated by

HQI = 1

HAI

HQI covers all the 9 generic features covered in the Guidance Document. The HQI class boundaries and corresponding WFD Quality Class are: 10

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primarily due to Shoreline Alteration (1a). As noted above, twelve water bodies were classed as moderate in HQI. Moderate HQI classification in Upper Liffey Estuary was driven by metrics 1a (Shoreline alteration), 2a (Barriers) 3b (Change in habitat) and 6a (Wave regime). In the Lee (Cork) Estuary Lower moderate classification in HQI is driven by metrics 1a (Shoreline alteration), 2a (Barriers), 3a (Change in habitat) and 7a (River flow). The majority of these metrics driving classification by HQI in these two water bodies were morphological. Using the HQI the hydrology in both Upper Liffey Estuary and Lee (Cork) Estuary Lower appears to be unimpacted. Results of the HQI were compared to the desk-based Trac-MImAS risk assessment methodology (RPS, 2015). The outcomes were generally similar with the same assessment in 13 of the areas assessed. Outcomes from TraC-MImAS were more morphology based and the HQI is more broadly based on hydromorphology. HQI appears to be less conservative than TraC-MImAS in the classification of these waterbodies. The 13 metrics used in HQI appear to reduce the effect of any one metric. In addition, HQI includes metrics measured regularly in the field leading to a greater confidence in the overall hydromorphological assessment.

in the calculation of the overall HQI score which is scaled appropriately. Hydromorphological integrity is central to the ecological structure and function of communities in transitional and coastal waters. With hydromorphology, an explicit component of the WFD, there is a need to understand the links between ecology and hydromorphology (Vaughan et al., 2009). As stated previously, however, there is a lack of quantitative data describing this relationship. (UKTAG, 2012; Orlando-Bonaca et al., 2012). The Environment Agency report (Environment Agency, 2009) outlines the direct and indirect linkages between hydromorphology and the six core WFD biological elements (phytoplankton, benthic invertebrates, fish, saltmarsh, seagrass and macroalgae) in transitional and coastal waters. Some biological elements are more sensitive to either hydrographic (e.g. phytoplankton) or geomorphological processes (e.g. saltmarshes), while most are responsive to the combination of hydro-geomorphological processes (e.g. benthic invertebrates) coupled with other environmental and biological forcing factors (e.g. seagrasses, fish) (Environment Agency, 2009). Determining whether and to what degree such inter-relationships exist is important for two reasons. First, it is vital to understand the importance of hydrogeomorphology to underpin good ecological status. Secondly, understanding these relationships is necessary to better measure and predict the effects of hydromorphological pressures and associated mitigation measures on WFD-relevant biota (Environment Agency, 2009). The need for baseline or unimpacted conditions is important in establishing a link between hydromorphology and ecology. This is challenging given the inherent variability in both physical habitat and biology (Vaughan et al., 2009; Bandelj et al., 2012). When determining the change in saltmarsh coverage, historic maps are used in the calculation of the total area that would be expected to be covered by saltmarsh if activities and alterations that impact on flooding dynamics were removed. This total area comprises current saltmarsh extent and the potential saltmarsh area (PSA). PSA includes area suitable for saltmarsh development based on interpretation of historic maps and verified using LiDaR data. Current extent of saltmarsh is determined by field survey (Devaney and Perrin, 2015). Dedicated research programmes are likely the only way to address many of the research questions linking hydromorphology to ecology. Another priority is to identify model systems or organisms that could act as research foci (Vaughan et al., 2009). Finally, the need to understand ecology–hydromorphology linkages is accentuated by the prospects of climate change and the subsequent sea level rise (Vaughan et al., 2009; Vogel, 2011). As well as looking at how hydromorphological changes can impact on biological functioning, the index has potential to be used in the designation and delineation of heavily modified water bodies. In Ireland, the designation of heavily modified water bodies in transitional and coastal waters in the first river basin management cycle followed the CIS guidance No. 4. (European Commission, 2000) which involved a stepwise identification of physical modification. This process did not consider the effects of modification on the ecology of the water bodies. The use of a categorical assessment scale will assist in deciding whether modifications are likely to impact on the ecology or if good ecological status can still be achieved despite the physical changes. While the development of the HQI has been undertaken using measured data, there is the potential to use the tool to assess changes from predicted variables. This will allow the testing of mitigation scenarios and their potential impact of ecological functioning. To date, WFD mitigation measures have been focused on restoring connectivity of habitats and enhancing movements of energy, material, and organisms (for rivers, this includes flow releases, sediment management, in channel habitat enhancement, connection to side branches). For marine systems such measures could be modelled using the HQI to predict likely outcomes. It can also be used to show that other impacts in water bodies may have the potential to affect the overall status. The HQI has allowed us to determine the likely status of hydromorphology across a diverse set of transitional and coastal waters

4. Discussion In this paper, we describe the development of an index for the classification of the hydromorphological condition of transitional and coastal waters. The new index improves on previous techniques by better representing the characteristics and features of transitional and coastal waters, by incorporating timelier field-based observations and by providing a numerical index that can quantify the magnitude of hydromorphological alteration. The WFD states that hydromorphology should be applied as a check for high status waters. However, there is a need too for a hydromorphological assessment method that assesses the extent of the impact in water bodies being damaged by hydromorphological pressures. There is also a need for a system to describe the magnitude and gradient of pressures. This is needed to assess the effects on hydromorphological and biological processes and to better prioritise measures. The five classes proposed here aligns with the concept and normative definition already used in the WFD. The development of this new tool, comprised of 13 metrics, describing the main features of transitional and coastal waters also provides a means to identify and address information gaps. Data for the development of HQI was from two main sources, a GIS spatial database of morphological alterations within Irish waters and WFD monitoring data, with the monitoring data sourced from surveys carried out on a regular basis. The GIS data layers used were developed for a variety of other uses, e.g. national habitats assessments, dumping at sea licensing and regulation and aquaculture licensing. These layers may need to be updated to be of use for assessing change. Future updates and amendments are particularly important to generate new data where there is currently no data, a lack of data, or where the current data is in places inaccurate (RPS, 2015). Ideally, all 13 metrics should be applied when calculating the HQI for a water body. Due to gaps in the available data this is not always possible. Metric 4a (change in the spatial extent of saltmarsh and seagrass beds), is applied in 13 water bodies. This reflects the fact that these biological quality elements are only found in certain water bodies (Devaney and Perrin, 2015; Wilkes et al., 2017). In the case of Metric 8a (change in dominant fraction particle size) data being gathered as part of the national WFD programme is patchy. Data is collected on a sixyear cycle and at present we do not have adequate data to look at change. This is the first application of the HQI. It has highlighted the gaps in the national data set. As more complete data sets for each water body become available and are incorporated into the analysis the number of metrics used in each water body analysis will increase. When scores for individual metrics are not available this is taken into account 11

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around the Irish coast. The outcome of the analysis is a tool which is of direct value and use to water managers in determining hydromorphological status of transitional and coastal waterbodies and will allow for more informed development of mitigation and restoration measures. Addressing hydromorphological pressures is a key part of River Basin Management planning. Furthermore, the HQI has the potential to be an important management tool in the designation process of HMWBs.

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