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The two-way exchange of water and properties such as heat and salinity as well as other suspended material between estuaries and the coastal ocean is important to regulating these marine habitats. This exchange can be challenging to measure. The Total Exchange Flow (TEF) method provides a way to organize the complexity of this exchange into distinct layers based on a given water property. This method has primarily been applied in numerical models that provide high resolution output in space and time. The goal here is to identify the minimum horizontal and vertical sampling resolutions needed to measure TEF depending on estuary type. Results from three realistic hydrodynamic models were investigated. These models included three estuary types: bay (San Diego Bay: data/SDB_*.mat files), salt-wedge (Columbia River: data/CR_*.mat files), and fjord (Salish Sea: data/SJF_*.mat files). The models were sampled using three different mooring strategies, varying the number of mooring locations and sample depths with each method. This repository includes the Matlab code for repeating these sampling methods and TEF calculations using the data from the three estuary models listed above. 

Saltwater intrusion (SWI) into coastal freshwater systems is a growing concern in the face of climate change‐driven sea level rise and hydrologic variability. Saltwater contamination of surface freshwater in the coastal California Pajaro Valley exemplifies this concern, where surface water cannot be diverted for agriculture if it is too saline. Closures at the mouth of the Pajaro River Lagoon, a bar‐built estuary in the Pajaro Valley, are associated with SWI. Closures and SWI are driven by a combination of offshore climate, coastal hydrodynamics, estuarine dynamics, inland hydrology, and infrastructure and management. Here, we describe the Pajaro Valley coastal water system and identify the oceanic and inland hydrologic drivers of SWI using available observational data between 2012 and 2020. We use time series and exploratory statistical analyses of coastal total water levels (TWLs), slough stage and salinity, river discharge, and contextual knowledge from local water managers. We observe that wet season lagoon closure and SWI events follow high oceanic TWLs coupled with low stage and discharge in the inland freshwater network, revealing how both wave and inland flow conditions govern lagoon closures and coincident SWI. This study yields novel empirical findings and a methodology for connecting coastal oceanography, estuarine coupled hydro‐ and morpho‐dynamics, inland hydrology, and water management practices relevant to climate change adaptation in human‐modified coastal water systems. 

Dry weather pollution sources cause coastal water quality problems that are not accounted for in existing beach advisory metrics. A 1D wave-driven advection and loss model was developed for a 30 km nearshore domain spanning the United States/Mexico border region. Bathymetric nonuniformities, such as the inlet and shoal near the Tijuana River estuary mouth, were neglected. Nearshore alongshore velocities were estimated by using wave properties at an offshore location. The 1D model was evaluated using the hourly output of a 3D regional hydrodynamic model. The 1D model had high skill in reproducing the spatially averaged alongshore velocities from the 3D model. The 1D and 3D models agreed on tracer exceedance or nonexceedance above a human illness probability threshold for 87% of model time steps. 1D model tracer was well-correlated with targeted water samples tested for DNA-based human fecal indicators. This demonstrates that a simple, computationally fast, 1D nearshore wave-driven advection model can reproduce nearshore tracer evolution from a 3D model over a range of wave conditions ignoring bathymetric nonuniformities at this site and may be applicable to other locations. 

Abstract Rainfall in southern California is highly variable, with some fluctuations explainable by climate patterns. Resulting runoff and heightened streamflow from rain events introduces freshwater plumes into the coastal ocean. Here we use a 105-year daily sea surface salinity record collected at Scripps Pier in La Jolla, California to show that El Niño Southern Oscillation and Pacific Decadal Oscillation both have signatures in coastal sea surface salinity. Averaging the freshest quantile of sea surface salinity over each year’s winter season provides a useful metric for connecting the coastal ocean to interannual winter rainfall variability, through the influence of freshwater plumes originating, at closest, 7.5 km north of Scripps Pier. This salinity metric has a clear relationship with dominant climate phases: negative Pacific Decadal Oscillation and La Niña conditions correspond consistently with lack of salinity anomaly/ dry winters. Fresh salinity anomalies (i.e., wet winters) occur during positive phase Pacific Decadal Oscillation and El Niño winters, although not consistently. This analysis emphasizes the strong influence that precipitation and consequent streamflow has on the coastal ocean, even in a region of overall low freshwater input, and provides an ocean-based metric for assessing decadal rainfall variability. 

Abstract Rip currents are generated by surfzone wave breaking and are ejected offshore inducing inner-shelf flow spatial variability (eddies). However, surfzone effects on the inner-shelf flow spatial variability have not been studied in realistic models that include both shelf and surfzone processes. Here, these effects are diagnosed with two nearly identical twin realistic simulations of the San Diego Bight over summer to fall where one simulation includes surface gravity waves (WW) and the other that does not (NW). The simulations include tides, weak to moderate winds, internal waves, submesoscale processes, and have surfzone width L sz of 96(±41) m (≈ 1 m significant wave height). Flow spatial variability metrics, alongshore root mean square vorticity, divergence, and eddy cross-shore velocity, are analyzed in a L sz normalized cross-shore coordinate. At the surface, the metrics are consistently (> 70%) elevated in the WW run relative to NW out to 5 L sz offshore. At 4 L sz offshore, WW metrics are enhanced over the entire water column. In a fixed coordinate appropriate for eddy transport, the eddy cross-shore velocity squared correlation betweenWWand NW runs is < 0.5 out to 1.2 km offshore or 12 time-averaged L sz . The results indicate that the eddy tracer ( e.g. , larvae) transport and dispersion across the inner-shelf will be significantly different in the WW and NW runs. The WW model neglects specific surfzone vorticity generation mechanisms. Thus, these inner-shelf impacts are likely underestimated. In other regions with larger waves, impacts will extend farther offshore. 

Land use and land cover (LULC) can significantly alter river water, which can in turn have important impacts on downstream coastal ecosystems by delivering nutrients that promote marine eutrophication and hypoxia. Well-documented in temperate systems, less is known about the way land cover relates to water quality in low-lying coastal zones in the tropics. Here we evaluate the catchment LULC and the physical and chemical characteristics of six rivers that contribute flow into a seasonally hypoxic tropical bay in Bocas del Toro, Panama. From July 2019 to March 2020, we routinely surveyed eight physical and chemical characteristics (temperature, specific conductivity, salinity, pH, dissolved oxygen (DO), nitrate and nitrite, ammonium, and phosphate). Our goals were to determine how these physical and chemical characteristics of the rivers reflect the LULC, to compare the water quality of the focal rivers to rivers across Panama, and to discuss the potential impacts of river discharge in the Bay. Overall, we found that the six focal rivers have significantly different river water characteristics that can be linked to catchment LULC and that water quality of rivers 10 s of kilometers apart could differ drastically. Two focal catchments dominated by pristine peat swamp vegetation in San San Pond Sak, showed characteristics typical of blackwater rivers, with low pH, dissolved oxygen, and nutrients. The remaining four catchments were largely mountainous with >50% forest cover. In these rivers, variation in nutrient concentrations were associated with percent urbanization. Comparisons across Panamanian rivers covered in a national survey to our focal rivers shows that saltwater intrusions and low DO of coastal swamp rivers may result in their classification by a standardized water quality index as having slightly contaminated water quality, despite this being their natural state. Examination of deforestation over the last 20 years, show that changes were <10% in the focal catchments, were larger in the small mountainous catchments and suggest that in the past 20 years the physical and chemical characteristics of river water that contributes to Almirante Bay may have shifted slightly in response to these moderate land use changes. (See supplementary information for Spanish-language abstract). 

Spatial and temporal carbonate chemistry variability on coral reefs is influenced by a combination of seawater hydrodynamics, geomorphology, and biogeochemical processes, though their relative influence varies by site. It is often assumed that the water column above most reefs is well-mixed with small to no gradients outside of the benthic boundary layer. However, few studies to date have explored the processes and properties controlling these multi-dimensional gradients. Here, we investigated the lateral, vertical, and temporal variability of seawater carbonate chemistry on a Bermudan rim reef using a combination of spatial seawater chemistry surveys and autonomous in situ sensors. Instruments were deployed at Hog Reef measuring current flow, seawater temperature, salinity, pH T , p CO 2 , dissolved oxygen (DO), and total alkalinity (TA) on the benthos, and temperature, salinity, DO, and p CO 2 at the surface. Water samples from spatial surveys were collected from surface and bottom depths at 13 stations covering ∼3 km 2 across 4 days. High frequency temporal variability in carbonate chemistry was driven by a combination of diel light and mixed semi-diurnal tidal cycles on the reef. Daytime gradients in DO between the surface and the benthos suggested significant water column production contributing to distinct diel trends in pH T , p CO 2 , and DO, but not TA. We hypothesize these differences reflect the differential effect of biogeochemical processes important in both the water column and benthos (organic carbon production/respiration) vs. processes mainly occurring on the benthos (calcium carbonate production/dissolution). Locally at Hog Reef, the relative magnitude of the diel variability of organic carbon production/respiration was 1.4–4.6 times larger than that of calcium carbonate production/dissolution, though estimates of net organic carbon production and calcification based on inshore-offshore chemical gradients revealed net heterotrophy (−118 ± 51 mmol m –2 day –1 ) and net calcification (150 ± 37 mmol CaCO 3 m –2 day –1 ). These results reflect the important roles of time and space in assessing reef biogeochemical processes. The spatial variability in carbonate chemistry parameters was larger laterally than vertically and was generally observed in conjunction with depth gradients, but varied between sampling events, depending on time of day and modifications due to current flow.