Using a three-dimensional, hydrostatic, primitive-equation ocean model, this study investigates the dynamics of lateral circulation in a partially stratified tidal inlet, the Barataria Pass in the Gulf of Mexico, over a 25.6-hour diurnal tidal cycle. Model performance is assessed against observational data. During flood tide, the lateral circulation exhibits the characteristics similar to that induced by differential advection, i.e., lateral flow consists of two counter-rotating cells and is convergent at the surface. The analysis of momentum balance indicates that, in addition to the pressure gradient and vertical stress divergence, nonlinear advection and horizontal stress divergence are also important contributors. During ebb phase, the lateral circulation is mostly eastward for the whole water column and persisting for almost the whole period. The surface divergence suggested by the differential advection mechanism lasts for a very short period, if it ever exists. The main momentum balance across most of the transect during ebb is between the along-channel advection of cross-channel momentum and pressure gradient. The sectional averaged lateral velocity magnitude during ebb is comparable to that during flood, which is different from the idealized numerical experiment result.

This work presents updated reconstructions of watershed runoff to San Francisco Estuary from tree-ring data to AD 903, coupled with models relating runoff to freshwater flow to the estuary and salinity intrusion. We characterize pre-development freshwater flow and salinity conditions in the estuary over the past millennium and compare this characterization with contemporary conditions to better understand the magnitude and seasonality of changes over this time. This work shows that the instrumented flow record spans the range of runoff patterns over the past millennium (averaged over five, ten, twenty and one hundred years), and thus serves as a reasonable basis for planning-level evaluations of historical hydrologic conditions in the estuary. Over annual timescales we show that, although median freshwater flow to the estuary has not changed significantly, it has been more variable over the past century compared to pre-development flow conditions. We further show that the contemporary period is generally associated with greater spring salinity intrusion and lesser summer-fall salinity intrusion relative to the pre-development period. Thus, salinity intrusion in summer and fall months was a common occurrence under pre-development conditions and has been moderated in the contemporary period due to the operations of upstream reservoirs, which were designed to hold winter and spring runoff for release in summer and fall. This work also confirms a dramatic decadal-scale hydrologic shift in the watershed from very wet to very dry conditions during the late 19th and early 20th centuries; while not unprecedented, these shifts have been seen only a few times in the past millennium. This shift resulted in an increase in salinity intrusion in the first three decades of the 20th century, as documented through early records. Population growth and extensive watershed modification during this period exacerbated this underlying hydrologic shift. Putting this shift in the context of other anthropogenic drivers is important in understanding the historical response of the estuary and in setting salinity targets for estuarine restoration. By characterizing the long-term behavior of San Francisco Estuary, this work supports decision-making in the State of California related to flow and salinity management for restoration of the estuarine ecosystem.

The estuarine exchange flow increases longitudinal dispersion of passive tracers and traps sinking particles, potentially creating an estuarine turbidity maximum (ETM): a localized maximum of suspended particulate matter concentration in an estuary. The ETM can have many implications - dead zones due to increased turbidity or hypoxia from organic matter decomposition, naval navigation challenges, and other water quality problems. Using timescales, we investigate how the interaction between exchange flow and particle sinking leads to ETMs by modeling a sinking tracer in an idealized box model of the Total Exchange Flow (TEF) first developed by Parker MacCready. Results indicate that the balance of particle sinking and vertical mixing is critical to determining ETM size and location. We then focus on the role of ecology in ETM formation through the use of The Peter-Parker Model: a new biophysical model which combines the TEF box model with a Nutrient-Phytoplankton-Zooplankton-Detritus (NPZD) model, the likes of which were first developed by Peter J.S. Franks. Detritus sinking rates similarly influence detritus peak concentration and location (an ETM), but detritus ETMs occur in a different location than the sinking tracer due to the influence of the biological factors which create a time lag of about 1 day. Lastly, we characterize the flow of the models with a dimensionless parameter that compares timescales and summarizes the dynamics of the sinking tracer in ETM formation and can be used across systems.

Anthropogenic development can strongly influence natural river processes, leading to environmental changes that negatively affect important habitats and biodiversity, and consequently reduce economically important natural resources. This study investigated the effects of salinity intrusion on the habitat of the clam Corbicula japonica in the Seomjin River estuarine zone. We employed the Environmental Fluid Dynamics Code (EFDC) model, which incorporates topographic data and hydrological changes, to simulate salinity concentrations. Two salinity measurement facilities were installed in Seomjin River estuarine and operated to optimize the EFDC model. The results show that reduced flow rates due to intake have a negligible impact on the increased salinity. Maintaining optimal salinity (15–20 psu) during neap tides at the Seomjin River Bridge requires constant high flow rates, which poses significant challenges. Saltwater stratification is identified as the primary cause of pronounced salinity stratification, particularly during neap tides. Addressing this issue through river discharge and intake facility operation is challenging. Structural measures, including riverbed restoration and underwater barriers, are recommended to improve resistance to seawater intrusion. Future research should aim to develop scenarios to reduce salinity concentrations, quantify the reduction efficiency, and propose region-specific measures.

Seagrass beds and salt marshes play a crucial role in preserving and restoring estuarine ecosystems, providing essential services such as carbon sequestration, water filtration, and habitat for diverse marine life. Mapping these areas, particularly in remote locations, is challenging but essential for effective conservation efforts. This study explores the use of drones equipped with multispectral cameras to map seagrass meadows and salt marshes in estuarine environments. The methodology involved composing images into a multilayer multidimensional dataset, performing exploratory data analysis and principal component analysis, and utilizing Random Forest supervised classification to generate detailed maps. Applied to a case study of the Mira River in southern Portugal, this approach achieved mapping accuracies as high as 94% with kappa values of 0.91. These results demonstrate the efficacy of drone-based multispectral imaging and advanced analytical techniques in accurately mapping and monitoring critical estuarine habitats, offering a valuable tool for conservation and restoration initiatives.

The Adyar Creek, a backwater estuary at the mouth of the Adyar River on the Coromandel Coast of the Bay of Bengal, represents a critical ecosystem facing mounting pressure from urbanization. This study employed high throughput 16S rRNA gene sequencing to characterize bacterial communities within the riverine, estuarine, and coastal sediments of Adyar Creek. Proteobacteria was the dominant phylum across most samples, with proportions ranging from 39.65% to 72.09%. Notably, the estuarine environment exhibited a distinct taxonomic profile characterized by a significant abundance of Firmicutes (47.09% of the bacterial population). Distinct bacterial classes were observed across sediment types: Alphaproteobacteria (30.07% - 34.32%) in riverine sediments, bacilli dominated estuarine sediments (40.17%), and Gammaproteobacteria (15.71%-51.94%) in coastal sediments. The most significant environmental factors influencing bacterial community composition across these samples were pH, salinity, phosphate, and nitrate. LEfSe analysis identified specific genera within the estuary, including Bacillus (20.26%), unclassified Paenibacillaceae (12.87%), Clostridium (3.81%), Gailella (3.17%), Paenibacillus (3.02%), Massilia (1.70%), Paraburkholderia (1.42%), and Pantoea (1.15%), as potential biomarkers for habitat health. Functional analysis revealed elevated expression of genes associated with ABC transporters and carbon metabolism in the estuary, suggesting a heightened nutrient cycling capacity. Furthermore, co-occurrence network analysis indicated bacterial communities exhibit a strong modular structure with complex species interactions across the three sediment types. These findings highlight bacterial communities' critical role and their key drivers in estuarine ecosystems, establishing a baseline for further investigations into the functional ecology of these vulnerable ecosystems.