Bathymetric flow rectification in a tropical micro-tidal estuary

Journal Pre-proof Bathymetric flow rectification in a tropical micro-tidal estuary David Salas-Monreal, Mayra Lorena Riveron-Enzastiga, Jose de Jesus Salas-Perez, Rocio Bernal-Ramirez, Mark Marin-Hernandez, Alejandro Granados-Barba PII:

S0272-7714(19)30828-5

DOI:

https://doi.org/10.1016/j.ecss.2019.106562

Reference:

YECSS 106562

To appear in:

Estuarine, Coastal and Shelf Science

Received Date: 23 August 2019 Revised Date:

9 November 2019

Accepted Date: 20 December 2019

Please cite this article as: Salas-Monreal, D., Riveron-Enzastiga, M.L., de Jesus Salas-Perez, J., Bernal-Ramirez, R., Marin-Hernandez, M., Granados-Barba, A., Bathymetric flow rectification in a tropical micro-tidal estuary, Estuarine, Coastal and Shelf Science (2020), doi: https://doi.org/10.1016/ j.ecss.2019.106562. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. © 2019 Published by Elsevier Ltd.

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Bathymetric flow rectification in a tropical micro-tidal estuary

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David Salas-Monreal1*, Mayra Lorena Riveron-Enzastiga2, Jose de Jesus SalasPerez3, Rocio Bernal-Ramirez4, Mark Marin-Hernandez1, Alejandro GranadosBarba1

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*Corresponding author: [email protected]

Universidad Veracruzana, Instituto de Ciencias Marinas y Pesquerías, Calle Hidalgo 617, Col. Río Jamapa, 94290, Boca del Río, Veracruz, México. Noordwijk International College, Blvrd del Mar 491, Boca del Rio, Veracruz C.P. 94299, MEXICO. Universidad Veracruzana, Facultad de Ciencias Biológicas y Agropecuarias. Carr. Tuxpan-Tampico km 7.5., Col. Universitaria, 92860, Tuxpan, Veracruz, México. Instituto Tecnologico de Mexico / Instituto Tecnologico de Boca del Rio, Carretera Veracruz-Cordoba km 12, Boca del Rio, Veracruz C.P. 94290, MEXICO.

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Abstract

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Temperature, salinity and current velocity data were recorded during the two principal

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atmospheric seasons affecting the tropical micro-tidal estuaries in the western Gulf of

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Mexico. Tropical micro-tidal estuaries in the western Gulf of Mexico share many

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characteristics, among them a narrow connection between the estuary and the adjacent

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continental shelf. Therefore, samples were taken during the dry (April, 2009) and the rainy

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(July, 2009) seasons, in order to elucidate the effect of the narrow connection between the

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estuaries and the continental shelf on flow dynamics. Due to the similarities between the

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tropical micro-tidal estuaries located in the western Gulf of Mexico, the Jamapa River

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estuary, a shallow estuary, with a narrow connection with the continental shelf and a ~5 m

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wide navigational channel, was used as a case study. During the dry season (April 15-17th,

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2009) there was a surface horizontal displacement of the salinity and the temperature front

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of ~2 km, while during the rainy season (July 22-24th, 2009) the salinity and temperature

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gradients were mainly observed in the vertical at ~1 m depth. In this particular case, there

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was a marked difference between the northern and southern part of the estuary, due to the

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presence of a second river discharge (Arroyo Moreno), which discharges always stays in

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the northern part of the estuary (shallow area) owing to the influence of the navigational

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channel on fluid dynamics. Finally, a cyclonic recirculation was observed at the estuary

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mouth area. According to model outputs, the recirculation was observed when the ratio

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between the mouth and the estuary width were below 0.4, otherwise (>0.4) the recirculation

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was not observed. This should be a general behavior for all tropical micro-tidal estuaries

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located in the western Gulf of Mexico.

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Keywords: Hydrographic variability; shallow micro-tidal estuaries; current rectification;

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Jamapa River estuary; Veracruz Reef System; cyclonic recirculation.

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1. Introduction

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Tidal processes in estuaries are one of the fundamental ways to exchange organic matter

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and pollutants in short periods of time (Allen et al., 1980; Savenije, 2006; Friedrichs, 2010;

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Salas-Monreal et al., 2018). However, in micro-tidal estuaries the subtidal exchange

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between the continental shelf and the estuary are responsible for the long-term exchange of

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organic matter, pollutants, plankton and nekton (Sheldon and Alber 2002; Salas-Monreal

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and Valle-Levinson, 2008; Kim and Park, 2012). Such exchanges could be driven by

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several mechanisms such as the wind, the gravitational circulation, the river discharges and

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the bathymetric features, among others. The vertical and lateral structure of the flow is the

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main responsible of mass exchange between the estuary and the continental shelf

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(Goodrich, 1988; Valle‐Levinson and Lwiza, 1995; Valle-Levinson, 2008). Therefore, the

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residence time of the estuary mainly depends on the amount of fresh water input, the wind

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velocity, salinity gradients and the shape and bathymetry of the area (Rasmussen and

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Josefson, 2002). In channelized estuaries with abrupt bathymetric changes such as hollows,

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the residence time increases due to the generation of eddies, which generate a bilateral

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circulation over the edges of the estuary (Salas-Monreal and Valle-Levinson, 2009; Cheng

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and Valle-Levinson, 2009). Eddy circulation in estuaries has been described with in situ

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data (Cloern et al., 1983; Geyer et al., 2000; Officer, 1981) and model outputs (Dalrymple

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et al., 1990; Spiteri et al., 2008). Eddies are important since they can trap organic matter,

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pollutants and organism for long periods of time, increasing the residence time of the area

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and modifying the ecological health of the estuary.

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The importance of larvae, nutrients, organic matter, sediment transport and water exchange

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between the western Gulf of Mexico and the estuaries (Lohrenz et al., 1997; Stumpf et al.,

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1993) was reinforced during the oil spill of 2000 in the northern Gulf of Mexico and the oil

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spill in Galveston Bay (Texas, USA) (McCrea‐Strub et al., 2011; Lin and Mendelssohn,

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2012). In general, the estuaries located in the western Gulf of Mexico share many

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characteristics, such as the shallowness of the area, the amount of fresh water input, micro-

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tidal ranges, water exchange with the Gulf of Mexico through narrow passages, and narrow

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navigational channels for those located near industrialized cities. In estuaries, gyres are

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commonly generated by current rectification due to the shape of the estuary (Storlazzi et al.,

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2006); these should be a common characteristic for most of the estuaries located in the

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western Gulf of Mexico, due to the wide-shallow area of the estuaries (wide / depth > 100),

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which connects through a narrow passage with the continental shelf. Thus, most of the

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estuaries located in the western Gulf of Mexico may be used as a case study to describe its

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general dynamics.

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In order to correctly describe the bathymetric effects on the dynamics of a shallow micro-

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tidal estuary, it is necessary to have high spatial and temporal resolution data series. Models

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are extremely useful to describe currents and mass exchange in shallow macro-tidal

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estuaries, due to the difficulty to obtain accurate spatial and temporal in situ data. Currents

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and mass exchange in shallow channelized estuaries, have previously been described using

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three dimensional models (Zhu et al., 2015; Salas-Monreal et al., 2018), those models need

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to accurately reproduce the vertical stratification produced between buoyant and salty water

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(Lesser et al., 2004). Thus, it is important to have vertical temperature and salinity profiles

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during the different stages of the tidal cycle (diurnal or semidiurnal), in order to have a

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good simulation of the mass exchange and the residual current pattern between the estuary

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and the continental shelf. Among all oceanographic models, the Regional Oceanic Model

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System (ROMS) has been successfully used to describe currents and channel dynamics in

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estuaries. It has been used to simulate river discharges, with and without the influence of

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tides in a shallow estuary and to describe the buoyancy effects on the circulation (Guo and

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Valle-Levinson, 2007). It has also been used to demonstrate, that the nonlinear advective

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acceleration term can be of the same order of magnitude as the pressure gradient and the

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bottom stress terms, in the along-channel momentum balance (Scully et al., 2009). ROMS

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has also been used to study the lateral circulation and to estimate sediment transport in

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estuaries (Chen and Sanford, 2009). The resuspension and deposition of matter are

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processes of particular importance in estuarine systems and arise mainly due to the

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presence of cyclonic and anticyclonic gyres, respectively. Therefore, the aim of this study is

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to describe the bathymetric effect on the dynamics of a shallow micro-tidal estuary located

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in the western Gulf of Mexico. The Jamapa River estuary (Fig. 1), a wide-shallow estuary

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(wide / depth > 100), with a narrow connection to the continental shelf (Fig. 1c) and a

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marked rainy season (Riveron-Enzastiga et al., 2016), will be use as a case study, due to its

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similarities with most estuaries located in the western Gulf of Mexico. The Jamapa River

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estuary has a closed area in its southern part (Fig. 1b), with a mean depth of 1 m and a

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narrow (~5 m) navigational channel of ~2 m depth, this area is mainly filled with buoyant

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water from the Jamapa River (Gonzalez-Vazquez et al., 2019). In its northern side (Fig. 1c),

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it has a surface constant freshwater input from Arroyo Moreno, creating brackish water at

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the junction with the estuary. Seven kilometers upstream Arroyo Moreno, where a

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thermoelectric facility is located, there is an almost constant 25 °C temperature and 0

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salinity. However, Arroyo Moreno only discharges ~10 m3 s-1 at the junction with the

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Jamapa River estuary, while the Jamapa River discharges are 5 times greater during the dry

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season and one order of magnitude greater during the rainy season (Riveron-Enzastiga et

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al., 2016; Perales-Valdivia et al., 2018; Gonzalez-Vazquez et al., 2019). Finally, another

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relevant feature of the Jamapa River estuary is the exchange matter between the estuary and

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the Veracruz Reef System (Salas-Monreal et al., 2019), a coral reef system composed by 50

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structures located off the Jamapa River estuary (Liaño-Carrera et al., 2019).

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2. Materials and methods

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Temperature, salinity and current velocity data were recorded during two diurnal tidal

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cycles (~49 h) on April (15-17) and July (22-24), 2009. Those months correspond to the

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dry (March-June), and rainy seasons (June-September), respectively (Avendaño-Alvarez et

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al., 2017). At least 10 repetitions were made with a towed ADCP at a constant velocity of

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~3 m s-1. The 1200-kHz vessel-mounted ADCP ping rate of 1 Hz was averaged every 10 s,

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yielding a horizontal resolution of ~30 m and a vertical resolution of 0.5 m. The 1200-kHz

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ADCP compass was calibrated using a global positioning system (GPS) following Trump

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and Marmorino (1997), finally tidal currents from the vessel-mounted ADCP were

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separated following Lwiza et al. (1991), in order to obtain the residual flow. All tidal

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signals below diurnal frequencies were removed using a low-pass cosine-Lanczos filter

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(Salas-Monreal and Valle-Levinson, 2009). Tidal and residual currents were rotated in

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order to plot the along and across-channel currents, respectively (red line from “I” to “II” in

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Fig. 1c).

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Temperature and salinity profiles were plotted along two transects, the first following the

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Jamapa River estuary (red line in Fig. 1c) with a total distance of ~5 km upstream from “I”

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to “II”, and the second transect was carried out along the Mandinga Lagoon (red line in Fig.

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1b) covering ~10 km from “V” to “VI”. Temperature and salinity data were taken every

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~500 m from the beginning of the transects. Additionally, a zigzag transect was performed

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from “II” to “I” and from “VI” to “V” in order to obtain the temperature and salinity fields

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along and across the estuary, as well as the current velocities along and across the estuary

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from point “II” to “I”.

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During each of the sampling period (dry and rainy season), drift buoys were released at the

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entrance of Mandinga Lagoon (Fig. 1b), no towed ADCP data were obtained at this

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location due to logistic issues. Thus, both the Eulerian and Lagrangian description of the

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flow were made.

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Finally, the three dimensional Regional Ocean Model System (ROMS) was used to obtain

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the residual velocities at the estuary. ROMS was also used to change the width of the

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estuary mouth, in order to understand the importance of such constriction on estuary

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dynamics. The free surface, hydrostatic, primitive equation model uses sigma coordinates

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in the vertical (Haidvogel et al., 2000) in order to increase the accuracy of the simulations.

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According to Robertson (2006), the semidiurnal baroclinic tides are well simulated with

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ROMS. In this study, ROMS was setup following the basic configuration described by

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Salas-Monreal et al. (2018), in order to elucidate the bathymetric effect on the estuary

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dynamics of a shallow micro-tidal estuary. The model domain has 40 x 80 grid points with

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5 sigma coordinates. The vertical resolution varies from <0.2 m in the shallow part of the

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estuary to ~1 m in the deepest part. The horizontal resolution grid points (125 x 125 m)

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were chosen since gyres are often masked by insufficient grid resolution (Lynch et al.,

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1995). The free surface elevation, which uses the “Flather condition” (Marchesiello et al.,

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2001), the salinity, temperature, and water velocities at each grid point were recorded at 0.5

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hourly intervals after the model had reached stability. Bottom stress was assumed to be a

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quadratic function of the bottom velocity with a drag coefficient of 2.5x10-3, as previously

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used in other shallow estuaries (Li, C., & O'Donnell, 1997; Valle-Levinson et al., 2004;

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Salas-Monreal et al., 2018). The tidally averaged potential and kinetic energy were

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calculated for each grid point. Once the normalized differences in energy from successive

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iterations were on the order of 10-3 or lower ((Ei+1-Ei)/Ei < 0.001), the model was

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considered stable; this occurred after 62 simulation days. The model was tidally forced at

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the continental shelf boundary using the amplitude and phases obtained by Salas-Perez et

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al. (2008). The form factor (F = (K1 + O1)/(M2 + S2)) classifies the estuary as diurnal (F >

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3), therefore it was necessary to recollect data for at least 25 h. The model was forced at the

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northern entrance (7 km upstream Arroyo Moreno in Fig. 1c) with a constant velocity of

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0.4 m s-1 and a temperature and salinity of 25 °C and 0, respectively. Those values were

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obtained with an hourly survey performed on July 20, 2009 from 10:00 am to 6:00 pm, at a

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fix location (19.111276°N; -96.142902°W). Upstream the Jamapa River, the model was

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forced with a constant velocity of 0.5 m s-1, and a temperature and salinity of 23 °C and 0,

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respectively. Most of the tropical estuaries located in the Gulf of Mexico (GoM) have a

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narrow connection with the GoM; therefore, ROMS was used to modify the width of the

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estuary mouth in order to describe the constriction effects on the flow and mass exchange

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between the estuary and the continental shelf.

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3. Results and discussions

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During the sampling performed on April 15-17, 2009 (dry season) the water temperature

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had a diurnal variation of 0.5 °C (Fig. 2), while the diurnal variation observed during the

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rainy season on July 22-24, 2009 had a higher range (~1 °C), attributed to mass exchange

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between the relatively cold river discharges, coming from the mountains (~5,600 m),

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during ebb periods and the warmer continental shelf water, mainly observed during flood

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periods. During the rainy season, the river discharges were 10 times greater than during the

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dry season. As observed on July 23, a strong river discharge (>450 m3 s-1) combined with

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southwestward winds, generated a sea level increase of up to 15 cm. The sea level

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increased due to the wind direction, which blocked the river outflow. The sea level increase

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produced a barotropic pressure gradient (Gonzalez-Vazquez et al., 2019), which favors

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river water intrusion toward Mandinga Lagoon (Fig. 1), thus, increasing the sea level at the

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entire estuary.

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In general, the temperature during April, 2009 seems to have a diurnal and a fortnightly

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synodic variability in the form of the Msf tidal constituent (Salas-Monreal et al., 2019),

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while during July, 2009 it only has a diurnal modulation (Salas-Perez et al., 2012), this

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could be attributed to the relatively strong river discharge, which mask the fortnightly

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synodic variability signal during July. Even the more evident diurnal or semidiurnal tidal

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signal may get mask during strong river discharges (Gonzalez-Vazquez et al., 2019) or low

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pressure (strong rain) events (Rojo-Garibaldi et al., 2018) in micro-tidal estuaries. Both

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temperature time series (Fig. 2), one located in the Jamapa River (19.099841°N; -

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96.108232°W) and the other in Mandinga Lagoon (19.046942°N; -96.073131°W), showed

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the same pattern, suggesting a direct influence of the Jamapa River discharges at the entire

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estuary during the rainy season and the presence of the continental shelf water at both

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locations during the dry season.

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3.1. Dry season

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The sea surface salinity values observed between flood and ebb periods have a horizontal

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displacement of ~2 km (Fig. 3a,b), this is the sea surface salinity variation at the estuary

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during the dry season. The Arroyo Moreno river always showed low salinity values (< 4)

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and high temperatures (>25 °C) (Fig. 3c,d). High temperatures were attributed to the

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atmospheric temperature effect on shallow water areas. In July, the air temperature

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oscillates around 35 °C, then the water temperature should increase by sensible heat

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transfer or land-water conduction of heat. As observed with the sea surface temperature

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during ebb periods (Fig. 3d), the outflow of Arroyo Moreno stays in the northern part of the

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estuary; this could be a bathymetric effect, since the navigational channel is located in the

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southern part of the estuary (Fig. 1), therefore the less dens water will mainly stay near the

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surface over the shallower (northern) part of the river (Wong, 1994).

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The vertical profiles of the salinity (Fig. 3e,f) suggested that this is a salt wedge estuary and

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not a vertically mixed estuary as suggested by Gonzalez-Vazquez et al. (2019). During both

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tidal stages the vertical stratification was observed from the entrance of the estuary (Fig. 3f)

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to a distance of ~3 (ebb) to ~4 km (flood) upstream (Fig. 3f,e), with a vertical salinity and

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temperature gradient of ~10 psu m-1 and ~1.3 °C m-1, respectively. This variation is greater

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than the one found in most of the estuaries located in the Gulf of Mexico (Kim & Park,

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2012; Zhu et el., 2015; Salas-Monreal et al., 2018) and around the world (Stumpf et al.,

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1993; Sheldon & Alber, 2002; Savenije et al., 2006; Guo & Valle-Levinson, 2007; Chen &

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Sanford, 2009; Valle‐Levinson, 2008). The relatively high vertical gradients were attributed

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to the influence of the Veracruz Reef System (VRS), a warmer-salty coral reef system

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located in the continental shelf outside the Jamapa River estuary (Fig. 1a). Along the

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estuary as we move upstream, there was a marked decrease of salinity (Fig. 3e,f) as

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expected due to river discharges. There is also a relatively high surface temperature area

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(Fig. 3g,h) located at ~1.5 km distance, this was attributed to Arroyo Moreno, which

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discharge buoyant-warmer water at this location.

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The effect of the channel (Fig. 1) was also observed with current velocities (Fig. 4a,b).

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During flood periods, current inflows were stronger in the southern part of the estuary,

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contrary to what could be expected due to Coriolis dynamics, where the stronger inflow

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should be observed over the northern part of the estuary. The strongest inflow (> 0.1 m s-1)

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was observed over the navigational channel (southern part of the estuary), while during ebb

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periods, the outflow was mainly observed over the relatively shallow and flat (northern)

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part of the estuary due to the transverse variability of the flow (Wong, 1994) and the

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discharges of Arroyo Moreno. The along-channel velocities were always below 0.2 m s-1

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(Fig. 4c,d), while the across-channel velocities were one order of magnitude smaller (< 0.05

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m s-1). During flood periods, there was a convergence of the flow, in agreement with the

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salinity field (Fig. 3e), reinforcing the idea that the near bottom inflow was able to reach up

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to ~4 km upstream, while the surface inflow only reached ~2 km upstream, this is mainly

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attributed to surface buoyant river discharges from Arroyo Moreno and the Jamapa River,

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which block the sea surface continental shelf water inflow at this location. The velocity

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differences, from surface to bottom, during flood periods (bottom inflows and surface

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outflows), maybe indicative of vertical mixing (Salas-Monreal et al., 2018), however, since

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the calculated Richardson Number (Ri), from the mouth to a distance of 4 km upstream,

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was always above 0.25 (Ri < ¼ are used to denote mixed conditions), and there was a

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relatively strong vertical salinity and temperature gradient, it could be assumed that there is

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no vertical mixing during the dry season (Fig. 5), thus, confirming the idea that this is a salt

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wedge estuary and not a vertically mixed estuary. Finally, even though the across-channel

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velocity was one order of magnitude smaller when compared to the along-channel velocity,

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its velocities increased during ebb periods (Fig. 4d) at a distance of ~1.5 km from the

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mouth (~0.04 m s-1), just where Arroyo Moreno is located, implying that Arroyo Moreno

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has a strong influence on the across-channel dynamics of the Jamapa River estuary, even if

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its discharges were one order of magnitude smaller than the one coming from the Jamapa

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River.

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One of the interesting features observed during ebb periods at 19.095°N; -96.12°W was the

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modification of the flow (Yellow Square in Fig. 4b). The modification of the flow

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generated a cyclonic recirculation, which was confirmed with the calculated vorticity

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(

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for the rest of the estuary. Therefore the shape of the estuary may create a cyclonic

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recirculation, favoring bottom nutrient and sediment resuspension, enhancing a high

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biological productivity area at this location and increasing the residual time.

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The southern part of the estuary (Fig. 1b), had a more uniform horizontal and vertical

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salinity and temperature gradient (Fig. 6). The horizontal salinity (Fig. 6a,b) and

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temperature (Fig. 6c,d) fields also suggested the importance of the channel on the dynamics

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of the estuary. The saltier-cooler water was observed over the channel, while the relatively

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less salty water was observed over the edges, where the highest temperatures were found

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due to the shallowness (> 1 m depth) of the area (solar irradiance). The vertical salinity

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(Fig. 6e,f) and temperature (Fig. 6g,h) profiles showed a relatively weak vertical gradient

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when compared to the northern Jamapa River estuary (Fig. 3), this could be attributed to

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low fresh water input and to the shape of the estuary (Fig. 1a), which favor the intrusion of

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the warmer and salty continental shelf water at this location.

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The two buoys released at 19.046942°N; -96.073131°W, during flood (Fig. 6c) and ebb

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periods (Fig. 6d) followed the channel. During the flood period one of the buoys was able

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to get into the estuary, to a position equivalent to the maximal area where the continental

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shelf water enters, as observed with the salinity and temperature fields. The second buoy

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was stranded after ~4 h at the coast. During ebb periods both buoys followed the

−

). The vorticity was one order of magnitude greater (x10-4 s-1) at this location than

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navigational channel, reaching the narrowest part of the area in less than 7 h. Thus, during

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both tidal periods, the buoys followed the navigational channel, as expected.

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3.2. Rainy season

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During flood periods, the continental shelf water (Fig. 7) was able to reach up to 1 km

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upstream at the surface and ~3.5 km near the bottom (Fig. 7e), while during ebb periods the

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surface salinity values showed buoyant water at the entire transect (Fig. 7f), as a

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consequence of stronger river discharges (Fig. 7f) when compared to the dry season. The

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near bottom salinity field had a horizontal displace of 0.5 km from flood to ebb periods,

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moving through a submerged promontory. Therefore, due to the velocities observed during

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this season (Fig. 8) it could be assumed that the wave velocity (

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same order or lower than the flow velocity (V), where ´ is the reduced gravity and H is the

290

surface (Hs) or bottom layer (Hb) depth. If this is the case, there could be a supercritical

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flow at the estuary, increasing nutrient and sediment resuspension at this location.

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However, after calculating the composed Froude Number (Salas-Monreal et al., 2019), the

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values obtained from the mouth of the estuary up to 4 km upstream were always below 1,

294

indicating a subcritical flow. Therefore, even if it is a micro-tidal estuary, with relatively

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strong river discharges (Fig. 2j), passing through a narrow passage (> 100 m wide) with a

296

vertical constriction (promontory), the along-channel velocity observed during ebb periods

297

was not strong enough to create a hydraulic jump. According to the theory of Stommel and

298

Farmer (1952), if the Froude Number is below 1, as it was the case for the Jamapa River

299

estuary, the salt wedge intrusion may exist.

300

During ebb periods, the sea surface salinity over the continental shelf (Fig. 7b) showed the

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influence of the estuarine water over the southern part of the mouth. This was mainly

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attributed to the shape of the estuary mouth, which has a land extension on its northern side,

303

favoring the estuarine water to move southward and perhaps to Coriolis dynamics which

304

also favor this pattern. The sea surface temperatures during flood periods (Fig. 7c,g)

305

showed a front located ~2.5 km upstream.

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During ebb periods (Fig. 7d,h) the effect of the channel was also depicted (Fig. 7d),

307

showing the Arroyo Moreno outflows (warmer water) over the northern part of the estuary,

´

,

) may be of the

308

due to current rectification owing to the presence of the channel (Wong, 1994). Therefore,

309

regardless of the season, the outflows of Arroyo Moreno during ebb periods could be

310

observed over the northern part of the estuary. This pattern favors a marked difference in

311

temperature and suspended matter (visually observed) between the northern and southern

312

part of the estuary, from the junction of Arroyo Moreno toward the entrance of Mandinga

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Lagoon.

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The surface current velocities also showed a front located ~2 km upstream during flood

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periods (Fig. 8a), in agreement with the temperature field. Thus, there is a marked

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difference regarding the intrusion of the continental shelf water, between the dry and the

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rainy season. During the rainy season the velocity increases its magnitude, reaching ~0.8 m

318

s-1 upstream and ~0.5 m s-1 at the mouth of the estuary. At the conjunction with Arroyo

319

Moreno, there was a marked southward current component (Fig. 8a,b) due to the increment

320

in volume fluxes from Arroyo Moreno. This increment could also be observed with the

321

vertical profiles of the across-channel velocity (Fig. 8c,d), which showed velocities of up to

322

0.08 m s-1. One of the marked differences between the dry and rainy season was the salinity

323

and temperature field observed over the southern part of the estuary (Fig. 1b). During the

324

dry season it always showed oceanic characteristics, while during the rainy season the

325

salinity decreases (Fig. 9a,b,e,f). However, since during flood periods, there is always

326

inflow from the northern part of the estuary (Fig. 8a), it could also be assumed that there is

327

a constant oceanic water exchange during a diurnal tidal cycle in the northern part of

328

Mandinga Lagoon (Fig. 9). During the rainy season, the lower temperatures and salinities

329

were always observed over the southern part of Mandinga Lagoon, this implied that the

330

buoyant water from the Jamapa River was not responsible for the low salinity and

331

temperature values observed at this location. Therefore, the decrement of the salinity and

332

temperature (Fig. 9) was associated with underground water, which emerges at Mandinga

333

Lagoon during the rainy season, owing to an increment of the freatic level (Neri-Flores et

334

al., 2014).

335

Sediment samples were taken during the rainy season in the Veracruz Reef System (VRS),

336

located outside the Jamapa River estuary (Fig. 10), in order to identify the area of influence

337

of the estuary. Sediment samples were separated in sand, silt and clays, and reported

338

according to their percentages. In general, sands represented up to 70% of total samples,

339

they were mostly located toward the sides of the Jamapa River estuary mouth. Silts

340

represented up to 28% of total samples and were located outside the Jamapa River estuary;

341

this was expected since silts are associated with terrigenous origin (Amstrong-Altrin et al.,

342

2015). Therefore the influence of the estuary was observed at a distance of 9 km from the

343

estuary mouth, this is the farthest sampled station. This value was in agreement with the

344

calculated ratio of curvature (Avendaño-Alvarez et al., 2019), where the influence of the

345

Jamapa River estuary was also estimated at a distance of ~8 km from the estuary. Finally,

346

clays represented less than 7% of total samples. Its highest concentration coincides with the

347

location where a semi-permanent anticyclonic gyre is located (Salas-Monreal et al., 2009),

348

enhancing the deposition of suspended matter. At this location, the formation of coral reefs

349

is inhibited (Lieaño-Carrera et al., 2019) mainly due to silts and clay deposition.

350 351

3.3. Residual flow and model outputs

352

Using the residual currents obtained during the rainy season (Fig. 11a), it could be observed

353

that the flow had an oceanward direction, as expected for estuaries with a strong river

354

influence. The relatively stronger residual flow observed upstream decreases as we move

355

downstream. The same pattern was observed during the dry season (figure not shown) with

356

weaker velocities. The residual velocity data showed a faster flow coming from the Jamapa

357

River than the one coming from Arroyo Moreno, as expected since the Jamapa River

358

discharges are 10 times greater than the once coming from Arroyo Moreno. The residual

359

flow coming from Arroyo Moreno stays in the northern part of the estuary, while the

360

discharges of the Jamapa River were observed at the southern part of the estuary, where the

361

navigational channel is located. Once the flow reaches a submerged (0.5 m depth) land

362

protection infrastructure located outside Mandinga Lagoon (Red line in Fig. 11a), the flow

363

was rectified, inducing the cyclonic recirculation at this location. The land protection

364

infrastructure is used as protection against natural erosion of the estuary mouth, and also to

365

protect the navigational channel used by local marinas. This is a common feature for all

366

estuaries located near industrialized cities in the western GoM, such as Laguna de

367

Terminos, Alvarado, Tamiahua and Laguna Madre, in Mexico, Corpus Christi, Matagorda

368

and Galveston in the USA, among others around the world.

369

Using the Regional Ocean Model System (ROMS) in order to elucidate the effect of the

370

land protection infrastructure over the cyclonic flow recirculation, it was observed that if

371



is greater than 0.4 then the recirculation was observed (where

is the length

372

of the land protection infrastructure or the natural structure of the estuary mouth), while if

373

the ratio is below 0.4 then the recirculation was not induced (Fig. 11c). This pattern could

374

also be expected for tropical micro-tidal estuaries with a narrow connection with the

375

continental shelf (

376

model, it could also be observed that for this particular estuary, in the absence of the land

377

protection infrastructure the cyclonic recirculation was not observed (Fig. 11b). This is

378

mainly due to the presence of Mandinga Lagoon which rectifies the Jamapa River flow

379

toward this location, thus, increasing buoyant fresh water within the southern part of the

380

estuary. Therefore, in most tropical micro-tidal estuaries, where

381

residence time of all suspended matter should be higher, due to the induced cyclonic

382

recirculation, than for those estuaries with a wider connection with the continental shelf.

<< estuary width). Using the residual velocities obtained from the



> 0.4 the

383 384

4. Conclusion

385

Current velocities, salinity and temperature fields were recorded in a tropical micro-tidal

386

estuary, in order to elucidate the effect of the ratio, between the estuary mouth and the

387

width of the estuary in flow dynamics. In situ data at the Jamapa River estuary, showed the

388

influence of the tides up to a distance of 4 km upstream, as well as the influence of the

389

diurnal and the Msf tidal signal during the dry season, while during the rainy season the Msf

390

signal was masked by the strong river discharges. The outflows of Arroyo Moreno, an

391

adjacent river located in the northern part of the estuary, always stays in the northern part of

392

the estuary due bathymetric effects, inducing a marked difference in the salinity and

393

temperature fields as we move southwards. Finally, the presence of a submerged (0.5 m

394

depth) land protection infrastructure located at the mouth of the estuary, generate a cyclonic

395

recirculation. This pattern should be observed at micro-tidal estuaries around the world

396

when the

397

observed.

"#





$"

< 0.6, otherwise the recirculation should not be

398 399

Acknowledgements

400

The authors would like to acknowledge the students and crew of the “R/V Justo Sierra”,

401

from the National Autonomous University of Mexico (UNAM), during the different stages

402

of the core collection, as well as the students of the University of Veracruz (Mexico) during

403

the ~48 h data collection along the estuary during April and July, 2009. Finally, the authors

404

would like to acknowledge the comments and suggestions of two anonymous reviewers,

405

since their comments increased the scientific content of this manuscript.

406 407

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408 409 410

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Figure captions:

552

Figure 1. a) Location of the Jamapa River estuary in the western Gulf of Mexico and its

553

affluent (0.1° ~ 11.11 km), as well as b) the Mandinga Lagoon (0.02° ~ 2.22 km) and c) the

554

Jamapa River estuary (0.005° ~ 0.5 km). The red lines I-II and V-VI, represents the

555

sampling transect during April 15-17 and July 22-24, 2009. The bathymetry of the area is

556

shown with blue contours. The maximum depth at Mandinga Lagoon was of ~2.5 m, while

557

at the Jamapa River it was of ~5 m.

558

Figure 2. a,b) The sea level amplitude, c,d) the 24 h low-pass filtered wind velocity, as well

559

as the sea surface temperature e,f) at the Jamapa River estuary (19.099841°N, -

560

96.108232°W) and g,h) Maninga Lagoon (19.046942°N, -96.073131°W), and i,j) river

561

discharges, during April and July, 2009. The black continuous lines show the trends of the

562

temperatures and river discharges. The red area represents the sampling period of April 15-

563

17 and July 22-24, 2009.

564

Figure 3. a,b) Sea surface salinity and c,d) temperature during the sampling period of April

565

15-17, 2009, as well as e,f) the salinity and g,h) temperature profiles along transect I-II

566

(0.005° ~ 0.5 km).

567

Figure 4. The upper panel a,b) shows the sea surface current velocities represented with

568

black arrows during the sampling period of April 15-17, 2009. The blue color in panels

569

(a,b) represents inflow areas while the red color represents outflow areas. The yellow

570

square (b) shows a recirculation area. The lower panel c,d) shows the along-channel

571

(arrows) and across-channel (contours) current velocities, along transect I-II. Positive

572

contour (blue) indicate northward flow, while negative values (red) indicate southward flow

573

(0.01° ~ 1.11 km).

574

Figure 5. a) The vertical shear of the horizontal along-channel velocity (s-1), b) the root

575

square of the Brunt-Vaisala frequency (s-1) and c) the Richardson Number, along transect I-

576

II, during the flood sampling period of April 15-17, 2009.

577

Figure 6. a,b) Sea surface salinity and c,d) temperature during the sampling period of April

578

15-17, 2009, as well as e,f) the salinity and g,h) temperature profiles along transect V-VI

579

(0.02° ~ 2.22 km).

580

Figure 7. a,b) Sea surface salinity and c,d) temperature during the sampling period of July

581

22-24, 2009, as well as e,f) the salinity and g,h) temperature profiles along transect I-II

582

(0.005° ~ 0.5 km).

583

Figure 8. The upper panel a,b) shows the sea surface current velocities represented with

584

black arrows during the sampling period of July 22-24, 2009. The blue color in panels (a,b)

585

represents inflow areas while the red color represents outflow areas. The lower panel c,d)

586

shows the along-channel (arrows) and across-channel (contours) current velocities, along

587

transect I-II. Positive contour (blue) indicate northward flow, while negative values (red)

588

indicate southward flow (0.01° ~ 1.11 km).

589

Figure 9. a,b) Sea surface salinity and c,d) temperature during the sampling period of July

590

22-24, 2009, as well as e,f) the salinity and g,h) temperature profiles along transect V-VI

591

(0.02° ~ 2.22 km).

592

Figure 10. Contours of the total percentages of sand, silt and clay obtained from the cores

593

on July, 2009 (0.05° ~ 5.55 km).

594

Figure 11. a) Residual current velocities (black arrows) obtained during the sampling

595

period of July 22-24, 2009, and b) the model (ROMS) residual current velocities obtained

596

without the presence of the submerged land protection infrastructure (red line in the upper

597

panel). c) The lower panel shows the vorticity calculated at the red square vs the ratio

598

between the width of the estuary mouth versus the width of the estuary (0.005° ~ 0.5 km).

599 600

Highlights: * Tropical micro-tidal estuaries in the western Gulf of Mexico share many characteristics, among them a narrow connection between the estuary and the adjacent continental shelf. Here an analysis of









showed that when these value was below 0.4

there was a cyclonic recirculation induced by lateral constriction. Otherwise, the cyclonic recirculation was not observed. * Insity data at the Jamapa River estuary, used as a case study of a tropical micro-tidal estuary, showed the influence of the tides up to a distance of 4 km upstream, as well as the influence of the diurnal and the Msf tidal signal during the dry season, while during the rainy season the Msf signal was mask by the strong river discharges. * The river outflows, always stayed in the northern (shallow) part of estuary due bathymetric effects, inducing a marked difference of the salinity and temperature from the north to the south part of the estuary. This should be a common pattern in most tropical micro-tidal estuaries, therefore, they maybe different organism and flora, such as mangroves from one side to the other side (north to south) part of the estuary. * There was a lateral and vertical salinity and temperature gradient during the dry season, while during the rainy season there was only a vertical gradient. This variation was greater than the one found in most of the estuaries located in the western Gulf of Mexico.

Dear Professor S. Mitchell. Editor of Estuarine, Coastal and Shelf Science. University of Portsmouth, Portsmouth, UK

Dear Professor Mitchell,

We the authors of the paper titled “Bathymetric flow rectification in a tropical microtidal estuary”, David Salas-Monreal, Mayra Lorena Riveron-Enzastiga, Jose de Jesus Salas-Perez, Rocio Bernal-Ramirez, Mark Marin-Hernandez, Alejandro GranadosBarba, declare that we do not have any conflict of interest with any organization or other people to publication this research as a research paper in the Journal of Estuarine, Coastal and Shelf Science.

Thank you for all your considerations Regards, David Salas-Monreal [email protected]