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Estuarine and coastal geomorphology, biogeochemistry, water quality, and coastal food webs in river-dominated shelves of the Gulf of Mexico (GoM) are modulated by transport processes associated with river inputs, winds, waves, tides, and deep-ocean/continental shelf interactions. For instance, transport processes control the fate of river-borne sediments, which in turn affect coastal land loss. Similarly, transport of freshwater, nutrients, and carbon control the dynamics of eutrophication, hypoxia, harmful algal blooms, and coastal acidification. Further, freshwater inflow transports pesticides, herbicides, heavy metals, and oil into receiving estuaries and coastal systems. Lastly, transport processes along the continuum from the rivers and estuaries to coastal and shelf areas and adjacent open ocean (abbreviated herein as “river-estuary-shelf-ocean”) regulate the movements of organisms, including the spatial distributions of individuals and the exchange of genetic information between distinct subpopulations. The Gulf of Mexico Research Initiative (GoMRI) provided unprecedented opportunities to study transport processes along the river-estuary-shelf-ocean continuum in the GoM. The understanding of transport at multiple spatial and temporal scales in this topographically and dynamically complex marginal sea was improved, allowing for more accurate forecasting of the fate of oil and other constituents. For this review, we focus on five specific transport themes: (i) wetland, estuary, and shelf exchanges; (ii) river-estuary coupling; (iii) nearshore and inlet processes; (iv) open ocean transport processes; and (v) river-induced fronts and cross-basin transport. We then discuss the relevancy of GoMRI findings on the transport processes for ecological connectivity and oil transport and fate. We also examine the implications of new findings for informing the response to future oil spills, and the management of coastal resources and ecosystems. Lastly, we summarize the research gaps identified in the many studies and offer recommendations for continuing the momentum of the research provided by the GoMRI effort. A number of uncertainties were identified that occurred in multiple settings. These include the quantification of sediment, carbon, dissolved gasses and nutrient fluxes during storms, consistent specification of the various external forcings used in analyses, methods for smooth integration of multiscale advection mechanisms across different flow regimes, dynamic coupling of the atmosphere with sub-mesoscale and mesoscale phenomena, and methods for simulating finer-scale dynamics over long time periods. Addressing these uncertainties would allow the scientific community to be better prepared to predict the fate of hydrocarbons and their impacts to the coastal ocean, rivers, and marshes in the event of another spill in the GoM.

Prediction of rapid intensification in tropical cyclones prior to landfall is a major societal issue. While air–sea interactions are clearly linked to storm intensity, the connections between the underlying thermal conditions over continental shelves and rapid intensification are limited. Here, an exceptional set of in situ and satellite data are used to identify spatial heterogeneity in sea surface temperatures across the inner core of Hurricane Sally (2020), a storm that rapidly intensified over the shelf. A leftward shift in the region of maximum cooling was observed as the hurricane transited from the open gulf to the shelf. This shift was generated, in part, by the surface heat flux in conjunction with the along- and across-shelf transport of heat from storm-generated coastal circulation. The spatial differences in the sea surface temperatures were large enough to potentially influence rapid intensification processes suggesting that coastal thermal features need to be accounted for to improve storm forecasting as well as to better understand how climate change will modify interactions between tropical cyclones and the coastal ocean. Significance Statement The connections between the underlying thermal energy in the ocean that powers tropical cyclones and rapid intensification of storms over continental shelves are limited. An exceptional set of data collected in the field as well as from space with satellites was used to identify spatial variations in sea surface temperatures across the inner core of Hurricane Sally (2020), a storm that rapidly intensified over the shelf. The spatial differences were due to the heat loss from the surface of the ocean as well as heat transport by shelf currents. The spatial differences were large enough to potentially influence how quickly storms can intensify, suggesting that coastal thermal features need to be accounted for to improve storm forecasting.

River plumes discharging into continental shelf waters have the potential to influence the distributions, predator-prey relationships, and thus survival of nearshore marine fish larvae, but few studies have been able to characterize the plume environment at sufficiently fine scales to resolve the underlying mechanisms. We used a high-resolution plankton imaging system and a sparse convolutional neural network to automate image classification of larval fishes, their planktonic prey (calanoid copepods), and gelatinous planktonic predators (ctenophores, hydromedusae, and siphonophores) over broad spatial scales (km) and multiple pulses of estuarine water exiting Mobile Bay (Alabama, USA) into the northern Gulf of Mexico from 9-11 April 2016. Fine-scale (1 m) plankton distributions were examined to analyze predator-prey relationships across 3 distinct plume regimes that varied by degree of wind-forcing and mixing rates. In calm wind conditions, the water column was highly stratified, and fish larvae and zooplankton were observed aggregating in a region of river plume-derived hydrodynamic convergence. As winds strengthened, the water column was subjected to downwelling and highly turbulent conditions, and there was decreasing spatial overlap between larval fishes and their zooplankton prey and predators. Our results indicate that high-discharge plume regimes characterized by strong wind-forcing and turbulence can rapidly shift the physical and trophic environments from favorable to unfavorable for fish larvae. Multiple pathways for both nearshore retention and advective dispersal of fish larvae were also identified. Documenting this variability is a first step toward understanding how high discharge events and physical forcing can affect fisheries production in river-dominated coastal ecosystems worldwide.

Exposure to extreme events is a major concern in coastal regions where growing human populations and stressed natural ecosystems are at significant risk to such phenomena. However, the complex sequence of processes that transform an event from notable to extreme can be challenging to identify and hence, limit forecast abilities. Here, we show an extreme heat content event (i.e., a marine heatwave) in coastal waters of the northern Gulf of Mexico resulted from compounding effects of a tropical storm followed by an atmospheric heatwave. This newly identified process of generating extreme ocean temperatures occurred prior to landfall of Hurricane Michael during October of 2018 and, as critical contributor to storm intensity, likely contributed to the subsequent extreme hurricane. This pattern of compounding processes will also exacerbate other environmental problems in temperature-sensitive ecosystems (e.g., coral bleaching, hypoxia) and is expected to have expanding impacts under global warming predictions., Exposure to extreme events is a major concern in coastal regions where human populations and stressed ecosystems are at risk to such phenomena. Here the authors show a marine heatwave on the continental shelf resulted from a novel set of compounding effects due to a tropical storm followed by an atmospheric heatwave.

Mudblister worms Polydora websteri bore holes into oyster shells, and oysters respond by secreting extra layers of shell, creating a mudblister. When shucked, mudblisters can burst and release anoxic mud. Thus, infestation devalues oysters, particularly on the half-shell market. This study quantified oyster condition index and worm abundances over 2 full growing seasons at commercial oyster farms on the US Gulf of Mexico coast, and our results indicate that oyster growth rate, manipulated through ploidy and stocking densities, had little effect on worm infestation. Larval spionid worms were found year-round. Larval abundances were slightly higher within than away from farms, and larval size distributions were skewed toward smaller larvae within the farms, suggesting that farms may be a source of larvae. Triploid oysters had higher or comparable condition index values to diploids, but during summer months, when worm infestation was high, worm infestation was not correlated with condition index. Previously infested shells deployed at farms became more infested than uninfested shells at moderate infestation levels, but re-infestation was influenced more by farm location than by previous infestation condition. Higher infestation at a farm with more variable salinity as well as higher infestation in 2017 when salinity was lower suggest that salinity may be a potential driver of mudblister worm infestation. Results indicate that oyster farmers on this coast should use desiccation to treat oysters for mudblister worms frequently during the summer, but that manipulating stocking density or ploidy is unlikely to be effective in preventing mudblister worm infestation.

Destructive coastal floods are commonly increasing in frequency and may be caused by global precipitation intensification. Such connections through climate, watershed, and river processes are poorly understood because of complex interactions in transitional fluvial-marine environments where flooding is caused by rivers, marine storm surge, or both in compound events. To better understand river floods along the fluvial-marine transition, we study watersheds of the northeastern Gulf of Mexico using long-term observations. Results show intensifying precipitation decreased precipitation-discharge lag times, increasing river-flood frequency and the likelihood of compound events in fluvial-marine transitions. This reduction in lag time occurred when the Atlantic Multidecadal Oscillation and El Niño Southern Oscillation began strongly affecting river discharge through the advection of moist air, intensifying precipitation. Along the fluvial-marine transition, compound events were largest in inland reaches. However, for inland reaches, compound event water levels did not exceed the floods caused solely by river flooding, the largest flood hazard in these systems. Our results demonstrate precipitation and river discharge play critical roles in coastal flooding and will likely escalate flooding as the climate continues to warm and intensify precipitation.

As tides propagate inland, they become distorted by channel geometry and river discharge. Tidal dynamics in fluvial-marine transitions are commonly observed in high-energy tidal environments with relatively steady river conditions, leaving the effects of variable river discharge on tides and longitudinal changes poorly understood. To study the effects of variable river discharge on tide-river interactions, we studied a low-energy tidal environment where river discharge ranges several orders of magnitude, the diurnal microtidal Tombigbee River-Mobile Bay fluvial-marine transition, using water level and velocity observations from 21 stations. Results showed that diurnal tidal attenuation was reduced by the width convergence in seaward reaches and height convergence of the landward backwater reaches, with the channel convergence change location ∼40-50 km inland of the bayhead and seaward of the largest bifurcation. River events amplified tides in seaward regions and attenuated tides in landward regions. This created a region of river-induced peak amplitude seaward of the flood limit (i.e., bidirectional-unidirectional current transition), allowing more tidal energy to propagate inland. Tidal currents were attenuated and delayed more by river discharge than water levels, making the phase lag dynamic. The river impacts on the tides were delineated longitudinally and shifted seaward as river discharge increased, ranging up to ∼180 km. Results indicated the longitudinal shifts of river impacts on tides in alluvial systems can be estimated analytically using the ratio of river discharge to tidal discharge and the geometric convergence of the system. Our simple analytical theory provides a pathway for understanding the tide-river-geomorphic equilibrium along increasingly dynamic coasts.

Changes in tropical cyclone intensity prior to landfall represent a significant risk to human life and coastal infrastructure. Such changes can be influenced by shelf water temperatures through the...

In stratified estuaries susceptible to wind mixing events, the changes in stratification have important implications for estuarine dynamics. Understanding the timescale associated with these mixing events and indirect wind impacts is dependent on estimating the restratification timescale. Bay-wide stratification observations, turbulence time series, and long-term data were examined to quantify the response mechanisms and restratification times in Mobile Bay. Observations showed moderate increases in stratification occurred over 2–3 days after the mixing event and were spatially variable. Turbulence data and model results that further highlight the period of returning stratification had changes in the relative contribution of tidal straining and gravitational exchange for the residual circulation in the estuary. Estimates of dissipation for the two ADVs averaged 2.6–3.1 × 10−5 m2 s−3 prior to the mixing event and increased to 1.4–8.5 × 10−4 m2 s−3 after the mixing event. These changes showed with increasing stratification; the turbulent dissipation decreased. These results highlight initial high returns in stratification are slowed over time as the exchange and mixing in the bay develop, and stratification returns to its premixed state.

Flow interactions between two inlets of Mobile Bay, Alabama, and the Gulf of Mexico are described with ship-mounted ADCP surveys obtained on consecutive days. These two inlets, Main Pass (MP) and Pass aux Herons (PaH), remain interdependent throughout the diurnal tidal cycle. A phase lag of 31.6° (~2.1 h) affects the diurnal tidal currents between the two openings in the lower Mobile Bay. Tidal discharge through each inlet exhibits a time lag, that results in a phase-dependent discharge ratio between the two inlets. Consequently, the magnitude and direction of exchange flows between the two inlets are time-dependent. Early in the rising tide, Mobile Bay receives seawater only through MP while simultaneously discharging estuarine water through PaH. During the beginning of falling tide, Mobile Bay receives seawater through PaH while simultaneously discharging estuarine water through MP. Net transports through MP and PaH during the study period are positive and negative, respectively. Thus, Mobile Bay receives seawater from the Gulf of Mexico through MP and discharges a portion of this seawater, along with estuarine water, to eastern Mississippi Sound through PaH. The characterization of magnitudes and spatial structures of exchange flows in the lower bay determine how buoyant suspended matter connects between the Gulf, Bay, and Sound.

The benthic impact of aquaculture waste depends on the area and extent of waste accumulation on the sediment surface below and around the farm. In this study we investigated the effect of flow on biodeposit transport and initial deposition by calculating a rough aquaculture “footprint” around an oyster aquaculture farm in the Damariscotta River, ME. We also compared a site under the farm to a downstream “away” site calculated to be within the footprint of the farm. We found similar sediment biogeochemical fluxes, geochemical properties and macrofaunal communities at the site under the farm and the away site, as well as low organic enrichment at both sites, indicating that biodeposition in this environment likely does not have a major influence on the benthos. To predict accumulation of biodeposits, we measured sediment erodibility under a range of shear stresses and found slightly higher erosion rates at the farm than at the away site. A microalgal mat was observed at the sediment surface in many sediment cores. Partial failure of the microalgal mat was observed at high shear velocity, suggesting that the mat may fail and surface sediment erode at shear velocities comparable to or greater than those calculated fromin situ flow measurements. However, this study took place during neap tide, and it is likely that peak bottom velocities during spring tides are high enough to periodically “clear” under-farm sediment of recent deposits.

Hurricane Michael in 2018 was one of the strongest storms to impact the coastal U.S. and was unusual given that it occurred in October (i.e., late in the hurricane season) and intensified over the ...

Using long-term records (~11 years) of salinity and 390 days of ADCP data, aspects of the estuary length and salinity flux were evaluated in Mobile Bay under a range of river discharge, tidal, and wind conditions. The temporal variability in the salinity structure was represented by the estuary length and showed a relationship of with respect to river forcing, similar to values reported in San Francisco Bay and Delaware Bay. Local wind forcing was observed to play a role in modifying this relationship, in which estuary length responded asymmetrically to along-channel winds with up-estuary winds, reducing the estuary length. To further explore potential salinity transport changes associated with the wind, a 1D salinity flux was calculated using the ADCP and salinity profile data. River discharge was the main forcing condition driving seasonal changes in salinity flux. At shorter time scales, the wind became a dominant forcing condition and drove large changes in the salinity flux during low-discharge periods. At all discharge levels, down-estuary wind conditions enhanced the shear and subtidal exchange. During up-estuary wind conditions, the two-layer flow was inhibited and reduced the exchange. These results indicate that in a shallow microtidal system, wind can play a large role in modifying the estuary length on scales comparable to the spring–neap changes observed in other systems.

Evaluating the role of long-term anthropogenic changes on dissolved oxygen (DO) in coastal systems is often a challenge due to variability in a system and measurement sensitivity to spatial and temporal trends. Physical processes can significantly modify the DO variability and act as a major driver of uncertainty when it comes to quantifying the bio-chemical changes associated with the DO budget. Stratification has been observed to be a dominant factor in controlling the hypoxic conditions that can develop in Mobile Bay, AL, a shallow highly stratified estuary prone to episodic hypoxia. Using CTD transect data and long-term water quality monitoring stations the variability of DO was examined throughout Mobile Bay. This study examined the physical drivers of these trends and highlighted the role stratification, temperature, and advection play in driving the bay wide variability. Under stable conditions, the spatial trend in Mobile bay will reflect the along-estuary gradient. When stable conditions don't occur due to random episodic mixing events and cross estuary exchange, the Bay can be driven by a number of factors: the along-estuary gradients, time since the previous mixing event, level of stratification, and biochemical oxygen demand. The combination of these elements provides an increased understanding of the complex dynamics driving low DO in this system. Long-term trends show the DO is decreasing in Mobile Bay based on changes in DO in the shipping channel, northern region, and Bon Secour region.

Estuarine-shelf exchange can drive strong gradients in physical and biogeochemical properties in the coastal zone and exert a significant influence on biological processes and patterns. Physical, biogeochemical, and plankton data from an across-shelf transect extending south of Mobile Bay, Alabama, in conjunction with regional time series data, were used to determine the relative importance of estuarine-shelf interactions on the physical-biological structuring of the shelf environment during fall conditions (i.e., well-mixed, low discharge). This period was also characterized by a relatively unique weather event associated with the remnants of Hurricane Patricia, which drove a meteorological flushing of estuarine water onto the shelf. Survey data indicated generally low N:P ratios across the shelf, with slightly elevated dissolved inorganic nitrogen in the Region of Freshwater Influence (ROFI) that extended approximately 30 km offshore. The ROFI had higher values of chlorophyll-a, diatom-specific production, marine snow, and primary productivity, with notable contributions from the larger size cells (>5 µm). Furthermore, stratification provided a niche opportunity for Trichodesmium sp. aggregates , a typically oligotrophic cyanobacteria, at the offshore edge of the ROFI. The lens of estuarine water may have limited the vertical extent to which this population was mixed, providing enhanced light availability relative to the well-mixed offshore conditions. Following the biogeochemical trend, the highest zooplankton abundances were also located within the estuarine outflow. While limited in spatial extent, the distinct geochemical and biological characteristics within the ROFI demonstrate the ecological impacts that estuarine-sourced waters can have during periods of generally low productivity in the Mississippi Bight.

The oceanographic community routinely collects time series data of hydrography, water current velocity, and other basic physical, chemical, and biological properties of the marine environment. Such data are essential for establishing baseline characteristics of marine and estuarine ecosystems. However, the task of taking the raw data files as downloaded from a variety of instruments from multiple manufacturers, and converting them into file formats that can be used to address specific research questions, can be highly complex and time consuming. To illustrate some of these complexities, we have thoroughly documented the data processing steps for a small coastal ocean observing system near Mobile Bay, Alabama, that has been in operation since 2004. Our goals were to produce documentation and data provenance in sufficient detail for full science reproducibility of all studies that use data from this system, provide a template for other ocean observation operations, and highlight a need for better recognition of the significant amount of time and expertise often required to do both the data processing and the documentation for long-term observational systems.

The recent emergence of satellite-based sea surface salinity (SSS) measurements provides new opportunities for oceanographic research on freshwater influence in coastal environments. Several products currently exist from multiple observing platforms and processing centers, making product selection for different uses challenging. Here we evaluate four popular SSS datasets in the Gulf of Mexico (GoM) to characterize the error in each product versus in-situ observations: Two products from NASA’s Soil Moisture Active Passive (SMAP) mission, processed by Remote Sensing Systems (REMSS) (40 km and 70 km); one SMAP 60 km product from the Jet Propulsion Laboratory (JPL); and one 60 km product from ESA’s Soil Moisture Ocean Salinity (SMOS) mission. Overall, the four products are remarkably consistent on seasonal time scales, reproducing dominant salinity features. Towards the coast, 3 of the 4 products (JPL SMAP, REMSS 40 km SMAP, and SMOS) show increasing salty biases (reaching 0.7–1 pss) and Root Mean Square Error (RMSD) (reaching 1.5–2.5 pss), and a decreasing signal to noise ratio from 3 to 1. REMSS 40 km generally shows a lower RMSD than other products (~0.5 vs. ~1.1 pss) in the nearshore region. However, at some buoy locations, SMOS shows the lowest RMSD values, but has a higher bias overall (>0.2 vs.

Opportunistic observations captured the coupled estuarine-shelf interactions as the Alabama coastal region transitioned from a period of low to flood river discharge conditions. The period of focus was 18 February to 10 April 2011 during which time a combination of in situ (water level, salinity and velocity) and remote sensing (ocean color) data provided information on the estuarine and shelf environment prior to, during, and post a major river discharge event that captured a relatively rare spatially synoptic view of the structural evolution of a discharge plume in response to changing forcing conditions. The discharge event generated major changes in the hydrographic conditions and forcing responses within the estuary and on the shelf. The resulting surface advected plume was observed for approximately two weeks, during which time the observed differences in shelf circulation were directly linked to the discharge plume and a plume bulge with anticyclonic circulation was identified at times throughout the event. The plume was exposed to a range of wind conditions which modulated the surface structure: downwelling winds elongated the plume structure and upwelling winds reversed and widened the plume. The influence of wind forcing, even during very low wind (

The velocity and hydrographic structure across Broad Sound, a north-south orientated subsystem of Casco Bay, ME that lacks continuous coastal boundaries, were characterized using velocity observations from two moorings in late summer/fall of 2013 and velocity and density observations from a repeat-transect ship survey conducted over a tidal cycle during the same period. At tidal time scales, the system is dominated by a barotropic semidiurnal standing wave with a west to east decrease in tidal amplitude and relatively minimal phase change across the majority of the transect. The stratification (vertical differences of 0.5–1.0 kg m−3) was generally laterally uniform and stronger during the flood phase which is hypothesized to result from stronger offshore stratification. The mean circulation had strong lateral shear with inflow over the deepest point in the bathymetric cross section and eastern slope and outflow over the western slope. There was also vertical shearing of the horizontal velocities with stronger northward (or northward trending) velocities at depth. The depth-averaged subtidal fluctuations were relatively small (∼2–3 cm s−1) and uncorrelated between mooring sites suggesting the vertically uniform current response associated with remote wind forcing is of limited importance. On the other hand, the depth-dependent velocity fluctuations at the subtidal time scale were, in large part (∼36–72%), driven by wind forcing. The net flux ratio, a means of quantifying the relative importance of the vertical and lateral shear in the flow field, was typically ∼0.44 indicating the structure of the local wind response favored vertically sheared flow.

Harmful Algal Blooms (HABs) of Karenia brevis have been documented along coastal waters of every state bordering the Gulf of Mexico (GoM). Some Gulf Coast locations, such as Florida and Texas, suffer from recurrent intense and spatially large blooms, while others such as Mississippi seem to rarely observe them. The main objective of this work is to understand the dynamics that led to the K. brevis bloom in Mississippi coastal waters in fall 2015. Blooms of K. brevis from the Florida Panhandle region are often advected westward towards the Mississippi-Alabama coast; however there is interannual variability in their presence and intensity in Mississippi coastal waters. The 2015 K. brevis bloom was compared to the 2007 Florida Panhandle K. brevis bloom, which showed a westward advection pattern, but did not intensify along the Mississippi coast. Cell counts and flow cytometry were obtained from the Mississippi Department of Marine Resources, Alabama Department of Public Health, Florida Fish and Wildlife Conservation Commission and The University of Southern Mississippi. Ocean color satellite imagery from the Moderate Resolution Imaging Spectroradiometer onboard the Aqua satellite was used to detect and delineate the blooms in 2007 and 2015. Two different regional applications of NCOM-Navy Coastal Ocean Model (1-km resolution NCOM-GoM/Gulf of Mexico and 6-km resolution NCOM-IASNFS/Intra Americas Sea Nowcast Forecast System) were used to understand the circulation and transport pathways. A Lagrangian particle tracking software was used to track the passive movement of particles released at different locations for both bloom events. Ancillary data (e.g., nutrients, wind, salinity, river discharge) from local buoys, monitoring stations and coincident oceanographic cruises were also included in the analysis. The blooms of K. brevis reached the Mississippi coast both years; however, the bloom in 2007 lasted only a few days and there is no evidence that it entered the Mississippi Sound. Two major differences were observed between both years. First, circulation patterns in 2015 resulting from an intense westward-northwestward that persisted until December allowed for continuous advection, whereas this pattern was not evident in 2007. Second, local river discharge was elevated throughout late fall 2015 while 2007 was below the average. Thus, elevated discharge may have provided sufficient nutrients for bloom intensification. These results illustrate the complex, but important interactions in coastal zones. Further, they emphasize the importance in establishing comprehensive HAB monitoring programs, which facilitate our understanding of nutrient and phytoplankton dynamics, and stress the importance for multi-agency cooperation across state boundaries.

Spring-time water column velocity data in 2011 and density data from a series of spring-time hydrographic surveys from 2008 to 2011 were used to examine the spatial variability of the circulation over the inner shelf of the Mississippi Bight off Mobile Bay. Spring-time depth-averaged currents were eastward at all sites, but the vertical profiles were different. East of Mobile Bay the along-shelf flow was eastward, with an offshore component at the surface and an onshore component at depth, indicative of upwelling circulation. West of Mobile Bay the along-shelf flow was also eastward, with a characteristic region of negative vertical shear in the upper layer of the water column. The deeper site had an across-shelf flow structure similar to the east sites, while the shallower site exhibited onshore flow throughout the water column. These spatial differences are attributed, in part, to the seasonally averaged effects of local wind forcing and discharge. In terms of wind forcing, the depth-averaged along-shelf current responded to along-shelf wind asymmetrically in favor of upwelling (more transport in upwelling than during downwelling). Thus, weak seasonal downwelling favorable wind conditions did not inhibit the velocity profiles from having upwelling circulation. West of Mobile Bay, negative vertical shears in the upper portion of the velocity profiles were consistent with the influence of freshwater discharge. This freshwater influence is supported with available chlorophyll-a data (as a freshwater proxy), which showed an enhanced freshwater influence west of Mobile Bay. In addition, across-shelf density data showed a shallow lens of freshwater west of Mobile Bay. These findings have implications for understanding the transport of river-derived nutrients on the Mississippi–Alabama shelf.

Bathymetric effects on tidal currents are investigated at Main Pass, which is the primary inlet of Mobile Bay, Alabama. A 12-h ship-mounted ADCP survey, which covered nearly one-half of the diurnal tide during flood conditions, included 24 repetitions. The resulting velocity data demonstrate significant tidal variability in the horizontal and vertical current structure between the ship channel and the shoals. The diurnal tidal flows, the dominant tidal forcing, are 72° (4.8 h) ahead of the water level throughout shallower areas of Main Pass, indicating near-standing wave conditions. Moving across the mouth, a phase lag (5.37° or 20 min) develops with the deep channel tidal currents lagging the shoal region. The vertical tidal structure is also modified across the mouth where near-bottom flows change their direction first in the ship channel, while near-surface flows change their direction first over the western shoal. This may be related to the seaward pressure gradient associated with the relatively large (~1715 m 3 /s) freshwater discharge or the discharge interaction with a nearby opening, Pass-aux-Herons. Current magnitudes over the shoals and in the ship channel vary by as much as 1 m/s. Flows at the east side of Main Pass, close to Mobile Point, behave oppositely to those in the rest of the transect during the survey. This inconsistent flow pattern is caused by an anticyclonic eddy that is triggered by flow separation at Mobile Point.

This project addresses the need for an expansion in the monitoring of marine environments by providing a detailed description of a low cost, robust, user friendly sonde, built on Arduino Mega 2560 (Mega) and Arduino Uno (Uno) platforms. The sonde can be made without specialized tools or training and can be easily modified to meet individual application requirements. The platform allows for internal logging of multiple parameters of which conductivity, temperature, and GPS position are demonstrated. Two design configurations for different coastal hydrographic applications are highlighted to show the robust and versatile nature of this sensor platform. The initial sonde design was intended for use on a Lagrangian style surface drifter that recorded measurements of temperature; salinity; and position for a deployment duration of less than 24 h. Functional testing of the sensor consisted of a 55 h comparison with a regularly maintained water quality sensor (i.e., YSI 6600 sonde) in Mobile Bay, AL. The temperature and salinity data were highly correlated and had acceptable RMS errors of 0.154 °C and 1.35 psu for the environmental conditions. A second application using the sonde platform was designed for longer duration (~3–4 weeks); subsurface (1.5–4.0 m depths) deployment, moored to permanent structures. Design alterations reflected an emphasis on minimizing power consumption, which included the elimination of the GPS capabilities, increased battery capacity, and power-saving software modifications. The sonde designs presented serve as templates that will expand the hydrographic measurement capabilities of ocean scientists, students, and teachers.

Hydrographic variability on the Alabama shelf just outside of Mobile Bay, a major source of river discharge into the Gulf of Mexico, is examined using time series of water column temperature and surface and bottom salinity from a mooring site with a depth of 20 m in conjunction with a series of across-shelf CTD surveys. The time series data show variability in a range of time scales. The density variation is affected by both salinity and temperature, with its relatively strong annual signal mostly determined by temperature and its year to year variability mostly determined by salinity. Seasonal mean structures of temperature, salinity, and density show a transition from estuarine to shelf conditions in which three regions with distinct seasonal characteristics in their horizontal and vertical gradient structures are identified. Correlation analysis with the available forcing functions demonstrates the influence of Mobile Bay on the variability at the mooring site. At low frequencies, river discharge from Mobile Bay has a varying influence on salinity, which is absent during the periods with unusually low discharge. At shorter synoptic time scales, both the estuarine response to the across-shelf wind stress and the shelf response to the along-shelf wind stress are significantly correlated with temperature/salinity variability: the former becoming important for the surface layer during winter whereas the latter for the bottom layer during both winter and summer. These forcing functions are important players in determining the estuarine–shelf exchange, which in turn is found to contribute to the shelf hydrographic structure.

We investigated the influence of climatic and environmental factors on interannual variations in juvenile abundances of marine fishes in a river-dominated coastal system of the north-central Gulf of Mexico, where an elevated primary productivity sustains fisheries of high economic importance. Fish were collected monthly with an otter trawl at three stations near Mobile Bay from 1982 to 2007. Fish sizes were used to isolate juvenile stages within the data set, and monthly patterns in juvenile fish abundance and size were then used to identify seasonal peaks for each species. The average numbers of juvenile fish collected during these seasonal peaks in each year were used as indices of annual juvenile abundances and were related to corresponding seasonal averages of selected environmental factors via a combination of principal components analysis and co-inertia analysis. Factors contributing the most to explain interannual variations in juvenile fish abundances were river discharge and water temper...

Sub-inertial across-shelf flows over the central mid-Atlantic Bight were examined using long-range CODAR SeaSonde type HF-radar surface velocities for the period August 2002 through February 2004. Across-shelf flow in this region was found to be episodic, with offshore flow occurring six times more often than onshore flow. Several recurring spatial patterns in offshore flow are identified, and two of these patterns emerge as statistically significant using empirical orthogonal functions. The most common type of offshore flow was a shelf-wide flow with events occurring throughout the year. The most energetic and well-defined shelf-wide flow events occurred during October through April, when the water column was less stratified. Other offshore flow patterns were more localized, with a flow at the bend or ‘point’ in the New Jersey coast being most common and most energetic. The offshore flow events identified here are capable of driving significant offshore transport, with more than one-third of offshore flow episodes having potential transport distances of greater than 14 km. In addition, clusters of multiple offshore flow events are shown to be capable of transporting near-surface material across much of the continental shelf.

Declines in shark populations have sparked researchers and fishery managers to investigate more prudent approaches to the conservation of these fish. As managers strive to improve data collection for stock assessment, fisheries-independent surveys have expanded to include data-deficient areas such as coastal regions. To that end, a catch series from a nearshore survey off Alabama was combined with data from a concurrent offshore survey with identical methodology to examine the depth use of sharks across the continental shelf (2–366 m). The combined data set contained 22 species of sharks collected from 1995 to 2008: 21 species in the offshore data set (1995–2008) and 12 species in the nearshore data set (2006–2008). Depth was a significant factor determining species' distributions, primarily for Atlantic sharpnose Rhizoprionodon terraenovae, blacknose Carcharhinus acronotus, and blacktip C. limbatus sharks. Blacknose sharks had the highest catch per unit effort (CPUE) in the middepth stratum (10–...

The instantaneous sea level determined at two sites in the Murderkill Estuary, a tributary of Delaware Bay, results from the superposition of temporal variability operating over different time and spatial scales. Over the relatively short tidal time scales, the semidiurnal tides that represent the dominant tidal constituents in lower Delaware Bay show a modest increase in tidal amplitudes from the bay mouth (Lewes, Delaware), up to Bowers Beach (the mouth of the Murderkill Estuary). However, as the tides propagate into the Murderkill Estuary, the semidiurnal constituents undergo heavy attenuation, resulting in a 48% reduction in tidal amplitude from Bowers to Frederica (approximately the extent of saline intrusion). The diurnal tide, on the other hand, experiences only a 25% reduction in amplitude. The limited tidal asymmetry that is observed may be a result of interaction between flows in the tidal channel and the adjacent salt marsh. At longer time scales, the subtidal sea level experiences no attenuation. The Murderkill Estuary thus behaves like a low pass filter to preferentially damp out high frequency sea level forcing from lower Delaware Bay. The subtidal volume flux in the Murderkill is highly coherent with the time rate of change of sea level, indicating that the Murderkill basically co-oscillates with Delaware Bay in a standing wave fashion over the subtidal time scale. This remote coupling controls more than 90% of the variance in subtidal sea level in the estuary. The surface slopes in the lower bay and the Murderkill Estuary are closely correlated with winds along the orientation of the two waterways, consistent with the effect of local wind on subtidal sea level.

Observations of surface velocity data from August 2002 to February 2004 were collected by a series of four long-range high-frequency (HF) radars along the coast of New Jersey. The shelf observations of the central Mid-Atlantic Bight (MAB) were compared to historical observations of surface flow characteristics in the area. The time-averaged spatial mean velocity of 4 cm/s in the down-shelf along-shelf direction and 3 cm/s in the offshore across-shelf direction compared very well to historical surface measurements in the study region. However, as the spatial resolution of the data set revealed, this simple measure masked significant spatial variations in the overall and seasonal mean flow structures. Three regions – the south bank of the Hudson Shelf Valley, the southern New Jersey inner shelf (LEO-15) region, and the region offshore of the Delaware Bay mouth (southwest corner) – had mean flows that favor offshore transport of surface water. In terms of temporal variability, maps of the principle axes showed that the across-shelf (minor) axis contribution was not insignificant in the surface layer ranging from 0.3 to 0.9 of along-shelf (major) axis and that there were seasonal differences in orientation and ellipticity. Analysis of the spatial changes in the temporal and spatial correlation scales over the shelf showed that shelf position, in addition to site separation, contributed to the differences in these properties. Furthermore, observations over the Hudson Shelf Valley region suggested that this was a region of transition in which the orientation of along- and across-shelf components begin to change.

Estuarine outflow plumes are important coastal processes whose variable nature can make it difficult to monitor using traditional ship-based surveys. This study used multiple ocean color sensors to track an estuarine outflow plume from the Chesapeake Bay in April 2003. Although, no in situ data are available for irrefutable proof, the patterns in ocean color observations in conjunction with meteorological data, strongly suggest that the observed phenomena is in fact an outflow plume. The ocean color data were brought into a geographic information system (GIS), so that various types of spatial analyses could be performed on the plume signature. The observed plume exhibited the typical dynamic response to winds in which the plume narrows and accelerates during downwelling favorable winds, and widens and advects offshore during upwelling favorable winds. Furthermore, area growth, and along- and across-shore frontal speeds of the plume were quantified and compared well to past in situ observations. Differences in the ocean color gradient field of the plume throughout the event were indicative of the expected evolution of the plume structure. This study demonstrates the importance of spatially comprehensive coverage of plume outflow events as well as the suitability of ocean color satellite remote sensing to monitor such events.

An algorithm for determining chlorophyll‐a concentrations in shallow, case II waters has been developed and applied to nearly six years of Sea‐viewing Wide Field‐of‐view Sensor (SeaWiFS) data in order to observe the general chlorophyll‐a patterns in a coastal estuarine environment. Due to the fact that the current empirical chlorophyll‐a algorithm (OC4) used to process SeaWiFS data breaks down in coastal waters, a neural network based algorithm was developed. The neural network in the study uses SeaWiFS remote sensing reflectance data paired with in situ chlorophyll‐a data in the Delaware Bay and its adjacent coastal zone (DBAC) from a number of different days and seasons in an effort to overcome the limitations of single day algorithms and simulated dataset algorithms. Although the neural network model (NN) in this study displayed some difficulty representing high chlorophyll‐a values, it showed significant improvement over the OC4 algorithm. The performance parameters of the NN were an r 2 of 0.79, a ro...

The exchange of coastal waters between the Mississippi Sound (MSS), Mobile Bay, and Mississippi Bight is an important pathway for oil and pollutants into coastal ecosystems. This study investigated an event of strong and persistent inflow of shelf waters into MSS and Mobile Bay during October 2015 by combining in situ measurements, satellite ocean color data, and ocean model predictions. Navy Coastal Ocean Model predicted high-salinity shelf waters continuously flowing into the estuarine system and forecasted low-salinity waters trapped inside the estuaries which did not flush out until the passage of tropical cyclone Patricia’s remnants in late October. The October 2015 chlorophyll-a anomaly was significantly low inside and outside the MSS for the 2003 to 2015 time series. Similar low-chlorophyll-a anomalies were only seen in 2003. The October 2015 mean in situ salinities were up to 8 psu higher than mean from 2007 to 2015, and some estuarine stations showed persistent salinities above 30 psu for almost a month in agreement with model predictions. October 2015 was associated with low fall seasonal discharge, typical of fall season, and wind which was persistently out of the east to southeast [45–180]°. These persistent wind conditions were linked to the observed anomalous conditions.

Identification of the spatial scale at which marine communities are organized is critical to proper management, yet this is particularly difficult to determine for highly migratory species like sharks. We used shark catch data collected during 2006–09 from fishery-independent bottom-longline surveys, as well as biotic and abiotic explanatory data to identify the factors that affect the distribution of coastal sharks at 2 spatial scales in the northern Gulf of Mexico. Centered principal component analyses (PCAs) were used to visualize the patterns that characterize shark distributions at small (Alabama and Mississippi coast) and large (northern Gulf of Mexico) spatial scales. Environmental data on temperature, salinity, dissolved oxygen (DO), depth, fish and crustacean biomass, and chlorophyll-a (chl-a) concentration were analyzed with normed PCAs at both spatial scales. The relationships between values of shark catch per unit of effort (CPUE) and environmental factors were then analyzed at each scale with co-inertia analysis (COIA). Results from COIA indicated that the degree of agreement between the structure of the environmental and shark data sets was relatively higher at the small spatial scale than at the large one. CPUE of Blacktip Shark (Carcharhinus limbatus) was related positively with crustacean biomass at both spatial scales. Similarly, CPUE of Atlantic Sharpnose Shark (Rhizoprionodon terraenovae) was related positively with chl-a concentration and negatively with DO at both spatial scales. Conversely, distribution of Blacknose Shark (C. acronotus) displayed a contrasting relationship with depth at the 2 scales considered. Our results indicate that the factors influencing the distribution of sharks in the northern Gulf of Mexico are species specific but generally transcend the spatial boundaries used in our analyses.

[1] Water column velocity and hydrographic measurements on the inner Alabama shelf are used to examine the flow field and its forcing dynamics during the Deepwater Horizon oil spill disaster in the spring and summer of 2010. Comparison between two sites provides insight into the flow variability and dynamics of a shallow, highly stratified shelf in the presence of complicating geographic and bathymetric features. Seasonal currents reveal a convergent flow with strong, highly sheared offshore flow near a submarine bank just outside of Mobile Bay. At synoptic time scales, the flow is relatively consistent with typical characteristics of wind-driven Ekman coastal circulation. Analysis of the depth-averaged along-shelf momentum balance indicates that both bottom stress and along-shelf pressure gradient act to counter wind stress. As a consequence of the along-shelf pressure gradient and thermal wind shear, flow reversals in the bottom currents can occur during periods of transitional winds. Despite the relatively short distance between the two sites (14 km), significant spatial variability is observed. This spatial variability is argued to be a result of local variations in the bathymetry and density field as the study region encompasses a submarine bank near the mouth of a major freshwater source. Given the physical parameters of the system, along-shelf flow in this region would be expected to separate from the local isobaths, generating a mean offshore flow. The local, highly variable density field is expected to be, in part, responsible for the differences in the vertical variability in the current profiles.