Water quality in the inshore Great Barrier Reef lagoon: Implications for long-term monitoring and management

Water quality in the inshore Great Barrier Reef lagoon: Implications for long-term monitoring and management

Marine Pollution Bulletin 65 (2012) 249–260 Contents lists available at SciVerse ScienceDirect Marine Pollution Bulletin journal homepage: www.elsev...

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Marine Pollution Bulletin 65 (2012) 249–260

Contents lists available at SciVerse ScienceDirect

Marine Pollution Bulletin journal homepage: www.elsevier.com/locate/marpolbul

Water quality in the inshore Great Barrier Reef lagoon: Implications for long-term monitoring and management Britta Schaffelke ⇑, John Carleton, Michele Skuza, Irena Zagorskis, Miles J. Furnas Australian Institute of Marine Science, PMB 3, Townsville MC, QLD 4810, Australia

a r t i c l e Keywords: Great Barrier Reef Water quality Monitoring Nutrients Chlorophyll Turbidity

i n f o

a b s t r a c t Coastal and inshore areas of the Great Barrier Reef lagoon receive substantial amounts of material from adjacent developed catchments, which can affect the ecological integrity of coral reefs and other inshore ecosystems. A 5-year water quality monitoring dataset provides a ‘base range’ of water quality conditions for the inshore GBR lagoon and illustrates the considerable temporal and spatial variability in this system. Typical at many sites were high turbidity levels and elevated chlorophyll a and phosphorus concentrations, especially close to river mouths. Water quality variability was mainly driven by seasonal processes such as river floods and sporadic wind-driven resuspension as well as by regional differences such as land use. Extreme events, such as floods, caused large and sustained increases in water quality variables. Given the highly variable climate in the GBR region, long-term monitoring of marine water quality will be essential to detect future changes due to improved catchment management. Crown Copyright Ó 2011 Published by Elsevier Ltd. All rights reserved.

1. Introduction Coastal areas around the world are under increasing pressure from human population growth, intensifying land use, urbanization and industrial development. As a result, increased loads of suspended sediment, nutrients and industrially produced pollutants such as pesticides and other chemicals enter coastal waters and lead to declines in estuarine and coastal marine water quality which are manifested as eutrophication and increased water turbidity. Many tropical coastal regions are now considered to be at great risk of pollution because of limited environmental management in the face of strong economic and population growth. However, after decades of decline, some areas along the coasts of wealthier countries, generally in the temperate northern hemisphere, are showing signs of water quality improvements due to significant regulatory and policy intervention over the last two decades (see e.g. Cloern, 2001; Nixon, 2009). The biological productivity of the Great Barrier Reef (GBR) is sustained by nutrients (e.g. nitrogen, phosphorus, silicate, iron), which are supplied by a number of processes and sources (Furnas, 2003; Furnas et al., 1997, 2011). These include upwelling of nutrient-enriched subsurface water from the Coral Sea, rainwater, fixation of gaseous nitrogen and freshwater runoff from adjacent catchments. Land runoff is the largest source of new nutrients to the inshore GBR (Furnas, 2003; Furnas et al., 2011) which are then transported into the GBR lagoon especially ⇑ Corresponding author. Tel.: +61 7 4753 4382; fax: +61 7 4772 5852. E-mail address: [email protected] (B. Schaffelke).

during monsoonal flood events (Devlin and Brodie, 2005; Devlin and Schaffelke, 2009). However, most of the inorganic nutrients used by marine plants and bacteria on a day-to-day basis come from recycling of nutrients already within the GBR ecosystem (Furnas et al., 2005, 2011). It is well documented that sediment and nutrient loads carried by land runoff into the coastal and inshore zones of the Great Barrier Reef (GBR) have increased several-fold since European settlement (Kroon et al., 2012). This increase has been implicated in the decline of coastal coral reefs and seagrass meadows (reviewed in Brodie et al., 2008, 2012). Concern about the negative effects of land runoff led to the formulation of the Reef Water Quality Protection Plan (Reef Plan) for catchments adjacent to the GBR World Heritage Area (Anon, 2003; updated in Anon, 2009a). The Reef Plan aims at improving land management with the primary goals: (i) to halt and reverse the decline in quality of water entering the Reef by 2013 and (ii) to ensure that by 2020 the quality of water entering the Great Barrier Reef from adjacent catchments has no detrimental impact on the health and resilience of the GBR. Extensive monitoring programs covering both marine waters and adjacent catchments (Anon, 2009b), have been established to assess the effectiveness of the Reef Plan’s implementation. The Reef Rescue Marine Monitoring Program (MMP) has been initiated in 2005 and provides physicochemical and biological data to measure the effects of changes in inputs from the GBR catchments on marine water quality and inshore ecosystems. Before the MMP, published information on water quality coastal and inshore areas of the GBR lagoon was limited to a handful of research studies (Cooper et al., 2007; Schaffelke et al., 2003 and

0025-326X/$ - see front matter Crown Copyright Ó 2011 Published by Elsevier Ltd. All rights reserved. doi:10.1016/j.marpolbul.2011.10.031

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references therein; Walker and O’Donnell, 1981). However, extensive water sampling throughout the GBR lagoon over the last 25 years has established typical concentration ranges of nutrients, chlorophyll a and other water quality parameters and described the occurrence of persistent latitudinal, cross-shelf and seasonal variations in these concentrations (Brodie et al., 2007; De’ath and Fabricius, 2008; Furnas et al., 1997). While concentrations of most nutrients, suspended particles and chlorophyll a are normally low, water quality conditions in the coastal and inshore zones can abruptly change and nutrient levels increase dramatically for short periods following disturbance events (wind-driven re-suspension, cyclonic mixing, river flood plumes; see e.g. Brodie et al., 2010; Devlin and Schaffelke, 2009; Furnas, 1989). These nutrients are generally rapidly taken up by pelagic and benthic algae and microbial communities (Alongi and McKinnon, 2005), supporting shortlived phytoplankton blooms and high levels of organic production (Furnas, 1989; Furnas et al., 2005). The purpose of this article is to describe the spatial and temporal distributions of marine water quality variables at MMP monitoring sites established in the inshore GBR lagoon and to explore the environmental or anthropogenic drivers of these distributions. This ongoing water quality monitoring program has the objectives to (i) obtain long-term time series against which future change in water quality can be measured in response to land management changes climatic events or other long-term systemic changes, and (ii) to provide environmental data for correlative analyses of coral reef status in inshore waters of the GBR. 2. Materials and methods 2.1. Sampling sites Twenty (20) sites distributed along the developed GBR coastline between 17 and 23°S were selected for monitoring. The sites were grouped in clusters extending down-current from the influence of significant regional rivers, generally close to inshore fringing coral reefs (Fig. 1). Site clusters were located adjacent to regional natural resources governance boundaries (Natural Resource Management (NRM) regions) based on major river catchments: the Wet Tropics (11 sites), Burdekin, Mackay Whitsunday and Fitzroy (3 sites each). The Wet Tropics region contains six significant rivers and has a monsoonal climate with a reliably recurrent summer wet season and relatively low inter-annual variability in rainfall and runoff (see Table S1 in the electronic Supplementary Content for river flow data). In contrast, the Burdekin and Fitzroy regions each contain one very large river, have a dry monsoonal climate and are characterized by high inter-annual variability in rainfall and flow, with major flood events occurring at intervals of several years to decades (Furnas, 2003). The Mackay Whitsunday NRM region has several small rivers and a mixed wet/dry tropical climate. Sampling was undertaken three times per year, generally in February, June and October. Here we report data from 15 sampling occasions between August 2005 and February 2011. 2.2. Direct water sampling and analyses At all 20 sampling sites, discrete water samples were collected from two (in water <10 m deep) to three (>10 m deep) depths through the water column with Niskin bottles. Sub-samples from the Niskin bottles were analyzed for dissolved inorganic nutrients (NH4, NO2, NO3, SRP), dissolved organic nitrogen, phosphorus and carbon (DON, DOP, DOC), particulate nitrogen, phosphorus and organic carbon (PN, PP, POC), suspended solids (SS), chlorophyll a and salinity. Salinity was determined with a Portasal Model 8410A

Salinometer (Guildline). As light permitted, a Secchi disc reading was taken at each site. Duplicate sub-samples for dissolved nutrients were immediately filtered through a 0.45 lm filter cartridge (Sartorius Mini Sart N) into acid-washed screw-cap plastic test tubes and stored frozen ( 18 °C) until later analysis ashore. DOC samples were acidified with 100 ll of AR-grade HCl and stored at 4 °C until analysis. Inorganic dissolved nutrient (NO2, NO3, SRP) concentrations were determined by standard wet chemical methods (Ryle et al., 1981) implemented on a segmented flow analyser (Bran and Luebbe, 1997). Analyses of total dissolved nutrients (TDN and TDP) were carried out using persulphate digestion of filtered water samples (Valderrama, 1981), which were then re-analysed for inorganic nutrients, as above. DON and DOP were calculated by subtracting the separately measured inorganic nutrient concentrations (above) from the TDN and TDP values. To avoid contamination during transport and storage, ammonium (NH4) concentrations were analysed at sea, immediately after collection using the OPA fluorometric method (Holmes et al., 1999). Dissolved organic carbon (DOC) concentrations were measured by high temperature combustion (680 °C) using a Shimadzu TOC-5000A carbon analyser. Duplicate sub-samples for particulate nutrients and chlorophyll a analysis were collected on pre-combusted glassfibre filters (Whatman GF/F) and stored at 18 °C. Particulate nitrogen (PN) was determined by high-temperature combustion using an ANTEK 9000 NS Nitrogen Analyser (Furnas et al., 1995). Particulate phosphorus (PP) is determined spectrophotometrically as inorganic P (Parsons et al., 1984) after digesting the particulate matter in 5% potassium persulphate (Furnas et al., 1995). Particulate organic carbon (POC) was determined by high temperature combustion (950 °C) using a Shimadzu TOC-V carbon analyser fitted with a SSM-5000A solid sample module. Inorganic C on the filters (e.g. CaCO3) was removed by acidification of the sample with 2 M hydrochloric acid. Chlorophyll a concentrations were measured fluorometrically using a Turner Designs 10 AU fluorometer after grinding the filters in 90% acetone (Parsons et al., 1984). Sub-samples for suspended solids (TSS) were collected on preweighed 0.4 lm polycarbonate filters (47 mm diameter). After filtration, filters were rinsed with a small amount of deionized water to remove salt. TSS concentrations are determined gravimetrically from the mass difference between loaded and unloaded filters after drying overnight at 60 °C. 2.3. Autonomous water quality loggers Instrumental water quality monitoring was undertaken at 14 coral reef monitoring sites (Fig. 1) using Eco FLNTUSB Combination Fluorometer and Turbidity loggers (WET Labs, Philomath, USA). The Eco FLNTUSB instrument simultaneously measures chlorophyll fluorescence, turbidity (optical backscatter) and in situ temperature. The fluorometer measures fluorescence from a number of chlorophyll pigments and their degradation products which are collectively referred to as ‘‘chlorophyll’’, in contrast to data from the direct water sampling which specifically measures ‘‘chlorophyll a’’. The loggers were set to record data at 10 min intervals. Each recorded data point is the average of a 50 sample measurement burst. Instruments were changed over approximately every 4 months. After retrieval, the loggers were cleaned, data downloaded and the raw instrumental records converted into actual units (lg L 1 for chlorophyll, NTU for turbidity, °C for temperature) according to standard procedures given by the manufacturer. Instrumental data were validated by comparison to chlorophyll a and suspended solids concentration in water samples manually collected at the instrument deployment site during each changeover (see Schaffelke et al., 2010).

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Fig. 1. Location of the 14 coral reef sampling sites (red symbols, deployment of autonomous water quality instruments and regular direct water sampling), and six open water sampling sites (yellow symbols, direct water sampling only). Boundaries of the Natural Resource Management (NRM) Regions are represented by colored catchment areas and the black line for marine boundaries. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

2.4. Data analyses Values for water quality parameters collected by direct water sampling at each site and sampling occasion are presented as depth-weighted water column means. Summary statistics of all available data (medians, means, 5th and 95th percentiles) were calculated for each monitoring site and season (dry season: May to October, wet season: November to April). Annual, seasonal and regional differences in water quality and all higher level interactions among these primary factors were determined by a balanced, three-way, fixed-factor, multivariate analysis of variance which employed permutation methods and was based on the Gower Metric association measure (PERMANOVA, Anderson et al., 2008). The factor ‘Year’ contained six levels (years 2005/06, 2006/07, 2007/08, 2008/09, 2009/10, 2010/11), the factor ‘Season’ contained two levels (wet and dry) and the factor ‘Region’ contained four levels (NRM regions – Wet Tropics, Burdekin, Mackay Whitsunday, Fitzroy). Water quality was defined by concentrations of chlorophyll a, total suspended solids, PN, PP, POC and DOC and the physical characteristics of temperature, salinity, and Secchi disc depth. Dissolved nutrients were not

included in the analysis as they are often highly variable at small spatial and temporal scales and unlikely to resolve existing spatial and temporal patterns. The Gower Metric was deemed the most appropriate resemblance measure as the water quality variables employed in the analyses are on different scales, there are not many zero values, and; the various physical and chemical variables should be given equal weight (e.g., equal differences between values have the same influence on association, regardless of scale). Subsequent to the MANOVA, the Gower Metric resemblance matrix was subjected to a multivariate multiple regression procedure to investigate relationships between the water quality variables and a set of explanatory variables (DISTLM, Anderson et al., 2008). The explanatory variables were:  Year and month of sampling.  Latitude (as a proxy for NRM region).  River proximity; the distance from each sampling station to the nearest river mouth to the south (in nautical miles).  River flow (average flow of the closest river to the south of each sampling station in the month before sampling (in ML d 1); data provided by the Queensland Department of Environment

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and Resource Management). For an overview of long-term annual river flow rates see Table S1 in the electronic Supplementary Content.  The total area of land cleared (in ha yr 1) as a measure for disturbance in the closest river catchment to the south in the year before sampling (Dept. Nat. Res., 1999a,b; Dept. Nat. Res. Mines, 2000, 2003, 2004, 2005, 2006; Dept. Nat. Res. Water, 2007, 2008a,b; Dept. Env. Res. Management, 2009, 2010).  Land used for grazing (pasture) and land used for crops (each in ha) in the closest river catchment to the south in the year before sampling. Land use data are not available for individual years and were calculated based on 1999 land use data (Brodie et al., 2003), adjusted by annual clearing rates (see references above).  An index of potential resuspension averaged over the two days prior to sampling, which was calculated using a wave period for water column mixing based on either a fetch-limited or duration-limited formula (Ozger and Sen, 2007) with a critical wave period for resuspension of Tc = (4pD/g)  0.5 where g = 9.8 ms 1 and D = station depth (m) (Booth et al., 2000). The distribution of each explanatory variable was examined prior to the regression analysis and either square root or log transformed where necessary. To determine the most appropriate regression model, all possible combinations of predictor variables were tested for model inclusion with both the more generous AIC (An Information Criterion) and more strict BIC (Bayesian Information Criterion) selection criteria. These criteria are calculated by essentially the same formula except that the BIC criterion imposes a more severe penalty for the inclusion of extraneous predictor variables. From each of the two lists of all possible models generated by the two selection processes, 20 models with the lowest criteria values were chosen. For each model selected using the AIC criterion a corresponding BIC value was calculated (and vice versa). AIC values were then plotted against the corresponding BIC values for the 40 models (20 from each selection process) and examined for overlap. The selected model ranked high in each selection process (second in AIC list and third in BIC list) and had relatively low values of both the AIC and BIC criteria (Fig. S1 in the electronic Supplementary Content). The results from the multivariate multiple regression procedure were represented in a series of two-dimensional, distance-based redundancy biplots in which the explanatory variables from the selected regression model were used to constrain the ordination. The critical probability level for significance testing was set a priori at 5% for all analyses. The water quality instruments recorded mean chlorophyll fluorescence and turbidity readings every 10 min. Daily means, which are presented in graphs, were used to calculate means over the whole monitoring period (October 2007 to February 2011) and by season (dry season: May to October, wet season: November to April). Overall mean values were compared to trigger values in the Water Quality Guidelines for the Great Barrier Reef Marine Park (GBRMPA, 2009). A turbidity trigger value (1.54 NTU) was derived by transforming the suspended solids trigger concentration in the Guidelines (2 mg L 1) using an equation based on a correlation of suspended solids concentrations in direct water samples and instrumental turbidity readings (see Schaffelke et al., 2009).

especially season (Table S2 in the electronic Supplementary Content). This data variability is further analyzed below. The majority of water quality parameters (all nitrogen species and organic carbon, PP, chlorophyll and suspended solids) had higher concentrations during the wet season at most sites (Table S2). Only dissolved phosphorus species were higher at most sites in the dry season. Secchi depth readings were lower in the wet season (greater turbidity). Higher concentrations of most parameters were also measured at sites close to river mouths and regularly exposed to monsoonal land run off (Fig. 2, Table S2), i.e., Dunk, Magnetic, Pine, and Pelican Islands. The latter site, near the mouth of the Fitzroy River, had the highest overall mean values for eight of the 12 water quality parameters. Green Island, the site furthest offshore, had the lowest mean values of the five particulate water quality parameters and DOC and the highest average Secchi depth reading. Dissolved inorganic nutrient concentrations were generally low at all sites, with the majority of the sites having median concentrations of NH4, NO3 and SRP, respectively, of less than 0.1 lM, with dry season concentrations often at or below the limit of detection. NO2 concentrations were mostly <0.01 lM (data not shown). Dissolved organic nitrogen, phosphorus and carbon species dominate the nutrient stocks in the inshore GBR lagoon. The mean concentrations of DON over all sites and times was 5.6 lM, which was about 70 higher than inorganic nitrogen species, and approximately 5 higher than PN (overall mean 1.2 lM). Overall mean DOC concentrations were 66 lM, 7 higher than overall mean concentrations of POC. These differences were less pronounced in the phosphorus species where the overall mean DOP concentration of 0.2 lM was approximately twice the mean concentrations of DIP and PP, respectively. The ratios of carbon, nitrogen and phosphorus add further information, when examined in comparison to the Redfield ratio (C106:N16:P1). DIN:SRP ratios, as an indicator for readily bio-available nutrients, were much lower than the Redfield ratio and clearly differed between the wet and dry seasons with overall, albeit highly variable, averages of 4:1 and 1:1, respectively (Table 1). In contrast, DON:DOP ratios exceeded the Redfield ratio 3–5 times, reflecting the dominance of DON over other nitrogen species. C:N:P ratios of particulate matter (seston; POC:PN:PP) were less variable and closer to the Redfield ratio (121:12:1). Redfield ratios of the total carbon and nutrient pools, TOC:TN:TP, were higher with a mean value of 254:22:1 (Table 1), reflecting the high values of both DON and DOC. Records from the in situ water quality instruments at the 14 inshore reef sites were available for October 2007 to February 2011 (see Table 2 for summary statistics). Chlorophyll and turbidity values were at most sites higher during the wet season. High turbidity values (i.e., above the GBR water quality guideline value) were recorded at the reef sites most exposed to river influence, similar to the suspended solids data from the less frequent direct water sampling, i.e. at Dunk, Magnetic, Pine and Pelican Island (Table 2; Table S2, electronic Supplementary Content). The instrument data also showed high mean turbidity at Snapper and Daydream islands (Table 2). Instrument-derived chlorophyll concentrations (from chlorophyll fluorescence) were also broadly comparable to the results obtained by direct water sampling. Sites with high mean chlorophyll concentrations (i.e., above the GBR water quality guideline value of 0.45 lg L 1) measured by both approaches were Daydream, Pine, Humpy and Pelican islands (Table 2, Table S2, electronic Supplementary Content). 3.2. Environmental drivers of inshore GBR water quality

3. Results 3.1. Spatial and temporal patterns in inshore GBR water quality Most water quality parameters measured by direct water sampling were highly variable between sites (Fig. 2) and times,

The multivariate analysis of variance revealed significant highlevel interactions between sampling years, seasons and regions indicating that the effects of each factor were not consistent across all levels of the other factors and, hence, no single factor can be considered in isolation (Table S3, electronic Supplementary Content). In

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Fig. 2. Summary of of water quality data over six sampling years (2005/06 to 2010/11) at 20 sampling sites in four regions of the Great Barrier Reef lagoon (see Fig. 1 for geographical locations of numbered sites). Boxes represent the interquartile range (25 to 75th percentiles), the horizontal line is the median, and the whiskers represent the data range. Secchi = Secchi depth, SS = suspended solids, PP = particulate phosphorus, PN = particulate nitrogen, POC = particulate organic carbon, NH4 = ammonium, NO3 = nitrate, DOP = dissolved organic phosphorus, DON = dissolved organic nitrogen, DOC = dissolved organic carbon, SRP = soluble reactive phosphorus. Sites are arranged by increasing distance to the nearest river south of the site.

the subsequent multivariate multiple regression analysis, the first two axes of selected the regression model (see Section 2) explained 91% of the variability in the fitted model and 36% of total variability in the data (Fig. 3). The particulate variables PN, PP, POC and SS were highly correlated with decreasing Secchi depth, while salinity and temperature were inversely correlated (Fig. 3). The sequential conditional tests indicated that 30% of the variation in the water quality data set was explained by the temporal explanatory variables, i.e., month of sampling (19%), river flow (5%), resuspension index (4%) and year of sampling (2%) (Fig. 4; Table S4, electronic Supplementary Content), highlighting the extremely variable climate of the Great Barrier Reef region. Most obvious is the clear separation of the data into wet season and

dry season groups (Fig. 4), mainly associated with the physical variables of temperature (higher in the wet season) and salinity (lower in the wet season) and to a lesser extent with higher concentrations of DOC during the wet season (Fig. 3). This separation was clearly correlated with the explanatory variables month, year and river flow (Fig. 4). The water quality data in the years with high river runoff were clearly separated during both the wet seasons (confidence ellipses in Fig. 4 for years 07 & 08, 08 & 09, 09 & 10) and the dry seasons following these extreme wet seasons (confidence ellipses in Fig. 4 for years 08 & 09, 09 & 10), compared to the earlier dry years (confidence ellipses in Fig. 4 for years 05 & 06, 06 & 07 in both seasons, and dry season 07 & 08 which preceded an extreme wet season).

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Table 1 Summary of annual mean and seasonal stoichiometry of organic carbon and nutrient stocks from direct water sampling at 20 Great Barrier Reef inshore lagoon sites from 2005–2011. Ratios are given separately for dissolved inorganic (DIN:SRP) and dissolved organic nutrients, particulate matter (POC:PN:PP) and total stocks (TOC:TN:TP). SD = standard deviation. Season

Mean ratio

SD

DIN:SRP

Dry season Wet season All year

1.2 4.0 2.2

1.1 4.0 2.9

DON:DOP

Dry season Wet season All year

80.5 55.6 71.0

135.9 32.6 109.2

POC:PN

Dry season Wet season All year

10.0 10.6 10.2

2.4 5.6 4.0

POC:PP

Dry season Wet season All year

120.0 117.9 119.2

37.4 65.5 50.4

PN:PP

Dry season Wet season All year

12.3 11.5 12.0

3.2 2.7 3.1

TOC:TN

Dry season Wet season All year

11.9 12.5 12.2

3.4 3.4 3.4

TOC:TP

Dry season Wet season All year

242.6 287.5 260.4

85.9 81.6 86.9

TN:TP

Dry season Wet season All year

22.0 23.8 22.7

9.9 7.2 8.9

Fig. 3. Two-dimensional biplot of the partial correlation coefficients of water quality variables with the primary axes from a distance-based redundancy analysis (dbRDA). The dbRDA was constrained by the statistically significant explanatory variables from a multivariate multiple regression analysis (DISTLM).

The spatial explanatory variables explained a smaller, albeit still significant, amount of the variation in the data, i.e., latitude (4%), proximity to closest river mouth (2%), catchment area used for crop cultivation (1%) and catchment area used for grazing (1%) (Fig. 5; Table S4, electronic Supplementary Content). The regional confidence ellipses overlap during both sampling seasons (Fig. 5), however, the water quality at sites associated with the dry tropical catchments (Burdekin and Fitzroy) was generally more variable, mainly due to the particulate water quality constituents (compare Fig. 3), which were highly correlated with latitude, river proximity and catchment area used for grazing.

The high temporal resolution of the instrument records allows for visual examinations of smaller-scale variability of chlorophyll and turbidity and a qualitative comparison to potential drivers of this variability, i.e. discharge of the nearest river and local wind speed. As examples, we present data from pairs of sampling sites bordering two NRM with contrasting climate patterns and discharge regimes, one close to river influence and one further offshore: Russell and Dunk islands in the Wet Tropics region(wet tropical climate), and Pelican and Barren islands in the Fitzroy Region (dry tropical climate). At all four sites, the time series showed seasonal cycles of chlorophyll fluorescence, with higher values during the summer, and very high values generally recorded after peaks in river discharge (Figs. 6 and 7). The distinct spike in chlorophyll values at Russell Island during the summer of 2009 was associated with a flood event that inundated this site (Fig. 6a).

Table 2 Summary of mean chlorophyll fluorescence (lg L 1) and turbidity (NTU) at 14 GBR inshore reef sites measured by continuously deployed WET Labs Eco FLNTUSB Combination Fluorometer and Turbidity Sensors. Data are averaged over all data available (October 2007 to February 2011) and by season (wet season = November to April; dry season = May to October). Bold print indicates overall mean values above Water Quality Guideline trigger values for the Great Barrier Reef Marine Park (GBRMPA 2009; see Section 2 for conversion of suspended solids trigger value to turbidity units). Region

Site

Chlorophyll (lg L

1

)

Turbidity (NTU)

Overall

Dry season

Wet season

Overall

Dry season

Wet season

0.34 0.20 0.33 0.27 0.33

0.45 0.25 0.37 0.34 0.43

2.28 0.95 1.08 0.73 2.45

2.38 0.84 0.97 0.61 2.30

2.10 0.96 1.04 0.72 2.45

Wet tropics

Snapper Is Fitzroy Is High Is Russell Is Dunk Is

0.39 0.22 0.35 0.30 0.37

(0.19) (0.16) (0.16) (0.16) (0.24)

(0.13) (0.14) (0.14) (0.09) (0.16)

(0.23) (0.18) (0.16) (0.20) (0.29)

(2.86) (1.52) (1.64) (1.55) (3.54)

(2.20) (0.42) (0.91) (0.29) (2.55)

(3.01) (1.90) (1.91) (2.04) (4.06)

Burdekin

Pelorus Is Pandora Magnetic Is

0.52 (0.23) 0.40 (0.16) 0.47 (0.32)

0.47 (0.21) 0.40 (0.13) 0.45 (0.32)

0.58 (0.26) 0.41 (0.17) 0.53 (0.33)

0.74 (1.65) 1.23 (2.73) 2.29 (4.01)

0.53 (0.14) 0.98 (0.72) 1.80 (1.65)

0.85 (2.43) 1.33 (3.70) 2.68 (5.36)

Mackay Whitsunday

Double cone Is Daydream Is Pine Is

0.44 (0.32) 0.49 (0.14) 0.62 (0.20)

0.37 (0.15) 0.46 (0.12) 0.60 (0.18)

0.52 (0.39) 0.55 (0.14) 0.67 (0.20)

1.50 (1.38) 2.24 (1.94) 3.17 (3.17)

1.35 (0.85) 1.73 (0.98) 2.44 (1.55)

1.56 (1.67) 2.44 (2.29) 3.51 (3.95)

Fitzroy

Barren Is Humpy Is Pelican Is

0.42 (0.26) 0.50 (0.24) 0.58 (0.40)

0.29 (0.14) 0.39 (0.13) 0.38 (0.20)

0.56 (0.28) 0.61 (0.28) 0.76 (0.47)

0.44 (0.57) 1.16 (1.92) 5.18 (7.89)

0.30 (0.33) 0.59 (0.74) 2.21 (3.25)

0.58 (0.71) 1.67 (2.55) 7.20 (9.31)

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Island was associated with a strong wind event immediately after the major 2008 flood of the Fitzroy River (Fig. 7a). Much higher and more variable turbidity values were recorded at Dunk and Pelican islands, which are close to the coast and to river mouths; however the highest spikes also occurred during flood events (Figs. 6b and 7b).

4. Discussion

Fig. 4. Biplot of a distance-based redundancy analysis emphasizing temporal patterns in the water quality data. Ellipses encompass 95% confident regions for the bivariate mean of stations sampled in each year. Dashed ellipses represent wet season sampling (November to April) and solid ellipses dry season sampling (May to October).

Fig. 5. Biplot of a distance-based redundancy analysis emphasizing spatial patterns in the water quality data. Ellipses encompass 95% confident regions for the bivariate mean of stations sampled in each NRM region. Dashed and solid ellipses as in Fig. 4

The two sites closer to river influence (Figs. 6b and 7b, Table 2) have generally higher chlorophyll values than the more offshore sites (Figs. 6a and 7a, Table 2), the difference being less pronounced at the two Wet Tropics sites. High turbidity at the clear-water sites (Russell and Barren islands) was also generally associated with summer flood events; turbidity values and variability outside those events were relatively small (Figs. 6a and 7a). A very large turbidity spike at Barren

The values of water quality parameters measured in the GBR inshore lagoon over five years were in a range expected from previous studies and generally followed previously recognized seasonal patterns with higher concentrations of most parameters (chlorophyll a, suspended solids and nutrient species) during the wet season and spatial patterns with higher concentrations closer to the coast (e.g., Cooper et al. 2007; De’ath and Fabricius 2010; Furnas et al. 1997, 2005; Schaffelke et al. 2003). The more frequent measurements by water quality instruments covered only two parameters (chlorophyll fluorescence and turbidity) but supported the clear seasonal and cross-shelf patterns. These seasonal and cross-shelf gradients were especially apparent for the particulate water quality parameters (suspended sediment, particulate nutrients and organic carbon). These particulate parameters are correlated with changes in GBR inshore coral reef community composition (Thompson et al., 2010; Uthicke et al., 2010) and especially turbidity was the best predictor of changes in a number of measures of coral reef community structure and function (Fabricius et al., 2012). We recorded the highest turbidity values at sites close to river influence, especially during summer flood events. At these sites, 10–30% of daily mean turbidity values were above a suggested threshold of 5 NTU, above which corals are likely to experience photo-physiological stress due to light limitation (Cooper et al., 2008). There are surprisingly few long-term and broad-scale water quality monitoring programs in other coral reef systems, especially in the Indo-Pacific, to compare with GBR water quality data. Water column concentrations of dissolved nitrogen were much lower at GBR inshore reef sites than in Bermuda (Boyer and Briceño, 2010), Biscayne Bay (Florida; Caccia and Boyer, 2005), Florida Bay (Boyer et al., 1999), the Florida Keys (Lirman and Fong, 2007), La Parguera (Puerto Rico, Hertler et al., 2009) and San Andrés Island (Caribbean Colombia, Gavio et al., 2010). However, soluble reactive phosphorus concentrations are generally higher in the GBR. Chlorophyll concentrations and turbidity/suspended solids levels at our sites were similar or higher than in Bermuda (Boyer and Briceño, 2010), Biscayne Bay (Caccia and Boyer, 2005) and the Florida Keys (Lirman and Fong, 2007) but lower than in Florida Bay (Boyer et al., 1999) and Puerto Rico (Hertler et al., 2009). Nitrogen to phosphorus ratios have been used as an indicator of relative N or P limitation of algae for many years (Redfield, 1958). Low ratios of DIN to SRP in the inshore GBR lagoon indicate high levels of bioavailable dissolved phosphorus relative to dissolved nitrogen, especially during the dry season. These ratios are generally higher in Bermuda (Boyer and Briceño, 2010), Florida Bay (Boyer et al., 1999) and Colombia (Gavio et al., 2010). Seasonal nitrogen inputs to the GBR lagoon during summer flood events are a significant water quality issue, because they support high phytoplankton production leading to increased chlorophyll concentrations, while for most other times of the year phytoplankton biomass is N-limited (Furnas et al., 2005). To date, it is unclear what the consequences of high SRP availability are, but it is possible that certain types of phytoplankton (e.g. N-fixing cyanobacteria such as Trichodesmium spp.) may benefit from these conditions. Ratios of carbon–nitrogen-phosphorus (119:12:1, C:N:P) in the particulate fraction (seston) were slightly elevated compared to the Redfield ratio (C106:N16:P1, Redfield 1958) and much higher than ratios estimated

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Fig. 6. Time series of daily means of chlorophyll (green line, lg L 1) and turbidity (brown line, NTU) time-series collected by Eco FLNTUSB instruments at (a) Russell and (b) Dunk islands in the Wet Tropics NRM Region. Additional panels represent daily discharge from the Russell-Mulgrave (a) and Tully (b) rivers (blue line, ML day 1  104) and daily wind speeds (grey line, km h 1) from weather stations at Innsifail (a) and Cardwell (b).

from Puerto Rico (Hertler et al., 2009). This indicates higher carbon concentrations than expected, most likely as detritus particles and marine snow which are more abundant in the inshore GBR compared to offshore waters (Fabricius et al., 2003). There are very few comparative data on the stoichiometry of dissolved and particulate nutrients in tropical shelf seas waters and it is premature to conclude whether the ratios found are unusual. Enhanced organic matter concentrations in marine systems can be a symptom of eutrophication (sensu Nixon, 1995)and we suggest that the inshore GBR is episodically eutrophic during flood plume events when very high levels of nutrients, chlorophyll and

organic matter are measured (see also Devlin and Schaffelke, 2009; Devlin et al., 2012). Some coastal and inshore reefs in the GBR and elsewhere show signs of degradation that are consistent with eutrophication and fine sediment accumulation (De’ath and Fabricius, 2010; Fabricius, 2005, 2011; Fabricius and De’ath, 2004). However, organic matter accumulation is complex, depending on both input and transformation processes as well as hydrodynamics. At present we can only speculate on how long the influence of a flood event lasts and how it is transmitted through the food web. Results to date indicate that flood-delivered fine sediment remains in the coastal zone for long after the event, leading

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Fig. 7. Time series of daily means of chlorophyll (green line, lg L 1) and turbidity (brown line, NTU) time-series collected by Eco FLNTUSB instruments at (a) Barren and (b) Pelican islands in the Fitzroy NRM Region. Additional panels represent daily discharge from the Fitzroy River (blue line, ML day 1  104) and daily wind speeds (grey line, km h 1) from the weather station at Yeppoon.

to recurring high turbidity events through wind-driven resuspension (Wolanski et al., 2008; Lambrechts et al., 2010; Fabricius et al., in review). Concentrations of water quality parameters are also dependent on water residence, which for the GBR lagoon are still debated as different approaches have delivered very different results. Hancock et al. (2006), Wang et al. (2007) and Choukroun et al. (2010) estimate residence times of weeks, indicating a well-flushed system, while Brinkman et al. (2002) and Luick et al. (2007) estimate much longer residence times of several months. Satellite imagery of flood plumes suggests residence times in the GBR coastal and inshore zones of several weeks (Schroeder et al., 2012) and episodic

transport of flood-borne material into the midshelf and outer shelf reef regions (Devlin and Schaffelke, 2009). However, the period of time materials such as sediments, nutrients and pesticides remain in the GBR lagoon is also determined by processes such as biological uptake and transformation, sedimentation and burial, resuspension and remineralisation, which are not yet fully quantified on a whole-of-GBR scale (Furnas et al., 2011). The variability of water quality parameters in the inshore GBR lagoon was influenced by a complex interplay of temporal and spatial factors, both inherent (e.g., summer vs. winter months, distance to river mouth) and extrinsic (e.g., differences in river flow, considered as a proxy measure for land run-off; or spatio-temporal

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differences in sediment resuspension which is a function of local wind speed and direction and site characteristics such as depth). It is no surprise that measures of land use such as the area for cropping or cattle grazing had only minor explanatory value because over the five year study period these did not change significantly (Dept. Nat. Res. 1999a,b; Dept. Nat. Res. Mines, 2000, 2003, 2004, 2005, 2006; Dept. Nat. Res. Water, 2007, 2008a,b; Dept. Env. Res. Management, 2009). Elevated nutrient concentrations in GBR inshore waters are mostly linked to extrinsic factors, e.g. nutrient release from wind-forced re-suspension of coastal sediments (Furnas et al. 1997; Ullman and Sandstrom, 1987; Walker and O’ Donnell, 1981) or nutrient inputs from river runoff (Devlin et al., 2001; Devlin and Brodie, 2005). End-of-river loads of sediments and nutrients are strongly flow dependent and in our analysis river flow was the second most important factor explaining the data variability. Flood events are of relative short duration (several weeks) but profoundly influence the inshore water quality, especially turbidity, for months afterwards (Fabricius et al., in review). Annual end-of-river loads of sediments and nutrients based on direct measurements are only now becoming available for the most important rivers draining into the GBR lagoon (Reef Water Quality Protection Plan Secretariat, in prep.) and future analysis of inshore water quality will benefit from these data. Kroon et al. (2012) estimate distinct regional differences not only in total end-of-river loads of sediments and nutrients but also in the anthropogenic contribution to these loads. The dry tropical catchments of the Burdekin and Fitzroy regions have the highest anthropogenic loads of suspended solids, particulate phosphorus and nitrogen, while dissolved inorganic nitrogen loads are highest from Wet Tropics catchments (Kroon et al., 2012). Regional differences are also apparent in the marine water quality, with generally higher and more variable values of many water quality parameters at sites influenced by the Burdekin and Fitzroy rivers. The instrument data (turbidity, chlorophyll fluorescence) were not subject to an analysis of environmental driving factors (we considered the time series of just over three years as too short) but the observed seasonal and cross-self patterns clearly reflect the above discussed inherent and extrinsic factors. The marked short term variability (days to weeks) illustrates the challenge to use a snap-shot sampling design, i.e. the 4 monthly direct water sampling in this study, to detect temporal changes and spatial differences. Because the instruments capture the short-term variability in water quality parameters they are likely to be better suited to construct water quality time series to measure future change against, albeit limited to only two water quality measures. Another challenge is the high inter-annual variability in rainfall and associated river runoff, which makes it difficult to construct a ‘baseline’ of inshore water quality. However, we are confident that this first 5.5 year period of intensive water quality monitoring in the inshore GBR has constrained a ‘base range’ of values as our sampling has covered highly variable river runoff conditions (from dry to extremely wet years). While we could explain about 40% of total variability in the data, we are mindful that other, at present difficult to parameterize, factors affect inshore GBR water quality, e.g., local tidal forcing, variability in the quantity and quality of adjacent riverine input of sediment and nutrients, and quality (e.g., grain size and composition) of marine sediments in the area surrounding the sampling sites. The ongoing management of human pressures on regional and local scales, such as nutrient runoff and overfishing, is vital to provide tropical marine ecosystems with the maximum resilience to cope with global stressors such as climate change (Bellwood et al., 2004; Carpenter et al., 2008; Marshall and Johnson, 2007; Mora, 2008). To achieve this, we need to better understand the complex responses and thresholds of coastal ecosystems to anthropogenic pressures including the sometimes unpredictable responses to management actions such as nutrient reduction

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