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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. 

We use an idealized numerical model to investigate the dynamics and fate of a small river discharging into the surf zone. Our study reveals that the plume reaches a steady state, at which point the combined advective and diffusive freshwater fluxes from the surf zone to the inner shelf balance the river discharge. At a steady state, the surf zone is well-mixed vertically due to wave-enhanced vertical turbulent diffusion and has a strong cross-shore salinity gradient. The horizontal gradient drives a cross-shore buoyancy-driven circulation, directed offshore at the surface and onshore near the bottom, which opposes the wave-driven circulation. Using a scaling analysis based on momentum and freshwater budgets, we determine that the steady-state alongshore plume extent (Lp) and the fraction of river water trapped in the surf zone depend on the ratio of the near-field plume length to the surf zone width (Lnf/Lsz) across a wide range of discharge and wave conditions, and a limited set of tidal conditions. This scaling also allows us to predict the residence time and freshwater fraction (or dilution ratio) in the steady-state plume within the surf zone, which range from approximately 0.1 to 10 days and 0.1 to 0.3, respectively. Our findings establish the basic dynamics and scales of an idealized plume in the surf zone, as well as estimates of residence times and dilution rates that may provide guidance to coastal managers. # Data from: Dynamics and scaling of a small river discharging into the surf zone [https://doi.org/10.5061/dryad.2280gb608](https://doi.org/10.5061/dryad.2280gb608) The present dataset includes the [COAWST model](https://www.usgs.gov/centers/whcmsc/science/coawst-a-coupled-ocean-atmosphere-wave-sediment-transport-modeling-system) outputs used to describe the dynamics and scaling of a small river discharging into the surf zone. ## File structure The data are structured as follows: 1. plume_scale.mat - Data of plume scales of all the cases, where * Hs: significant wave height [m] * Q: river discharge [m^3 s^-1] * L_nf: near-field plume length [m] * L_p: alongshore plume extent [m] * h_sz: water depth at the surf zone edge [m] * x_sz: surf zone width [m] * S_in: inflow salinity [PSU] * g_p: reduced gravity at the river mouth [m s^-2] * g_p*_*0: reduced gravity at the river mouth calculated using the density difference between river inflow and ambient ocean water [m s^-2] * Eta_0: water surface elevation anomaly at the river mouth [m] * V_sz: total volume of freshwater trapped in the surf zone [m^3] * T: the time required for the plume to reach a steady state [day] * L_t: plume turning distance [m] * S_bar: averaged salinity in the plume [PSU] 2. DepthAveraged.mat - Depth-averaged flow fields. DepthAveraged_BaseCase.mat, DepthAveraged_Case1.mat, DepthAveraged_Case3.mat, DepthAveraged_Case4.mat, DepthAveraged_Case6.mat, DepthAveraged_Case7.mat, DepthAveraged_Case8.mat, DepthAveraged_Case9.mat, DepthAveraged_Case16.mat, DepthAveraged_Case17.mat, DepthAveraged_Case18.mat, DepthAveraged_Case19.mat includes the results of the base case, cases 1, 3, 4, 6-9, and 16-19, respectively. In these files: * Wetdry_mask: wet/dry mask on RHO-points [binary] * Wetdry_mask_u: wet/dry mask on U-points [binary] * Wetdry_mask_v: wet/dry mask on V-points [binary] * Z: free-surface [m] * S: surface salinity [PSU] * Hs: significant wave height [m] * U: vertically integrated u-momentum component [m s^-1] * U_st: vertically-integrated u-Stokes drift velocity [m s^-1] * V: vertically integrated v-momentum component [m s^-1] * V_st: vertically-integrated v-Stokes drift velocity [m s^-1] 3. FullField_BaseCase.mat - 3D flow fields for the base case, where * Z: free-surface [m] * S: salinity [PSU] * Hs: significant wave height [m] * Lw: mean wavelength [m] * U: u-momentum component [m s^-1] * U_st: u-Stokes drift velocity [m s^-1] * V: v-momentum component [m s^-1] * V_st: v-Stokes drift velocity [m s^-1] * W: w-momentum component [m s^-1] * W_st: w-Stokes drift velocity [m s^-1] * Aks: salinity vertical diffusion coefficient [m^2 s^-1] * Akv: vertical viscosity coefficient [m^2 s^-1] * Cs_r: S-coordinate stretching curves at RHO-points [-] * Cs_w: S-coordinate stretching curves at W-points [-] 4. FreshwaterTrace_BaseCase.mat - Time series of freshwater volume and fluxes for the base case, where * i_sz: XI-index of the location of the surf zone edge [-] * i_shore: XI-index of the location of the shoreline [-] * Vsz: volume of freshwater in the plume in the surf zone [m^3] * Vis: volume of freshwater in the plume in the inner shelf [m^3] * Vsz_total: total volume of freshwater in the surf zone [m^3] * Vis_total: total volume of freshwater in the inner shelf [m^3] * R2SZ_flux: freshwater flux discharging into the surf zone [m^3 s^-1] * Vchannel: volume of freshwater in the plume in the river channel [m^3] * Vchannel_total: volume of freshwater in the river channel [m^3] * SBoundary_flux_SZ: the freshwater fluxes through the southern domain boundaries of the surf zone [m^3 s^-1] * SBoundary_flux_IS: the freshwater fluxes through the southern domain boundaries of the inner shelf [m^3 s^-1] * NBoundary_flux_SZ: the freshwater fluxes through the northern domain boundaries of the surf zone [m^3 s^-1] * NBoundary_flux_IS: the freshwater fluxes through the northern domain boundaries of the inner shelf [m^3 s^-1] * WBoundary_flux: the freshwater fluxes through the westhern domain boundary [m^3 s^-1] 5. DepthAveraged_XDiagnostic.mat - Depth-averaged diagnostic output of cross-shore momentum terms. DepthAveraged_XDiagnostic_BaseCase.mat includes the results of the base case at the steady state, and DepthAveraged_XDiagnostic_0day_1mWave.mat includes those at the start of river flow. In these files: * ubar_xadv: time-averaged 2D u-momentum, horizontal XI-advection term [m s^-2] * ubar_yadv: time-averaged 2D u-momentum, horizontal ETA-advection term [m s^-2] * ubar_xvisc: time-averaged 2D u-momentum, horizontal XI-viscosity term [m s^-2] * ubar_yvisc: time-averaged 2D u-momentum, horizontal ETA-viscosity term [m s^-2] * ubar_prsgrd: time-averaged 2D u-momentum, pressure gradient term [m s^-2] * ubar_zqsp: time-averaged 2D u-momentum, quasi-static pressure [m s^-2] * ubar_zbeh: time-averaged 2D u-momentum, Bernoulli head [m s^-2] * ubar_bstr: time-averaged 2D u-momentum, bottom stress term [m s^-2] * ubar_wbrk: time-averaged 2D u-momentum, wave breaking term [m s^-2] 6. DepthAveraged_YDiagnostic_BaseCase.mat - Depth-averaged diagnostic output of alongshore momentum terms, where * vbar_xadv: time-averaged 2D v-momentum, horizontal XI-advection term [m s^-2] * vbar_yadv: time-averaged 2D v-momentum, horizontal ETA-advection term [m s^-2] * vbar_xvisc: time-averaged 2D v-momentum, horizontal XI-viscosity term [m s^-2] * vbar_yvisc: time-averaged 2D v-momentum, horizontal ETA-viscosity term [m s^-2] * vbar_prsgrd: time-averaged 2D v-momentum, pressure gradient term [m s^-2] * vbar_zqsp: time-averaged 2D v-momentum, quasi-static pressure [m s^-2] * vbar_zbeh: time-averaged 2D v-momentum, Bernoulli head [m s^-2] * vbar_bstr: time-averaged 2D v-momentum, bottom stress term [m s^-2] * vbar_wbrk: time-averaged 2D v-momentum, wave breaking term [m s^-2] 7. grid.zip - Model grid file. * This grid file is designed for use with [ROMS](https://www.myroms.org/index.php), the hydrodynamic module of the COAWST modeling system. A diagram illustrating how the variables are placed on the grid and where the boundaries lie relative to the grid is available on [WikiROMS](https://www.myroms.org/wiki/Grid_Generation). * This grid file is in NetCDF format, which can be opened and used by a wide range of application software such as MATLAB, Python, and Panoply. For more detailed information, please refer to its [official website](https://www.unidata.ucar.edu/software/netcdf/). ## Code/Software All the post-processing scripts and data are prepared by MATLAB. 

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. 

Abstract Numerous eddies in the coastal ocean may experience distortion due to interactions with the ambient flow. Here we investigate how coastal submesoscale eddy distortion affects the cross‐shore and vertical tracer transport using a high‐resolution, wave‐current coupled model in the La Jolla Canyon region within the Southern California Bight. Model dye is released representing freshwater discharges. Model validations show that the coupled model has weaker stratification and weaker currents. Analyses primarily focus on an eddy‐induced cross‐shore dye transport event. The results show that, the coastal eddy is squeezed in the alongshore direction and extends in the cross‐shore direction, driving cross‐shore dye transport. Along a mid‐shelf boundary, the total cross‐shore transport is found to be dominated by the along‐boundary perturbation flow, which is linked to the eddy distortion. In addition, this coastal eddy also possesses vigorous vertical motions. The vertical velocity is more negative on the eddy northern side, favoring local dye subduction. This N‐S vertical velocity asymmetry may largely be induced by the topographic beta effect and the weaker modeled stratification may strengthen this effect. Overall, coastal eddy distortion contributes to the offshore tracer transport and induces spatially non‐uniform vertical dye flux. 

Abstract We use an idealized numerical model to investigate the dynamics and fate of a small river discharging into the surf zone. Our study reveals that the plume reaches a steady state, at which point the combined advective and diffusive freshwater fluxes from the surf zone to the inner shelf balance the river discharge. At a steady state, the surf zone is well mixed vertically due to wave-enhanced vertical turbulent diffusion and has a strong cross-shore salinity gradient. The horizontal gradient drives a cross-shore buoyancy-driven circulation, directed offshore at the surface and onshore near the bottom, which opposes the wave-driven circulation. Using a scaling analysis based on momentum and freshwater budgets, we determine that the steady-state alongshore plume extent (L_p) and the fraction of river water trapped in the surf zone depend on the ratio of the near-field plume length to the surf-zone width (L_nf/L_sz) across a wide range of discharge and wave conditions and a limited set of tidal conditions. This scaling also allows us to predict the residence time and freshwater fraction (or dilution ratio) in the steady-state plume within the surf zone, which ranges from approximately 0.1 to 10 days and from 0.1 to 0.3, respectively. Our findings establish the basic dynamics and scales of an idealized plume in the surf zone, as well as estimates of residence times and dilution rates that may provide guidance to coastal managers. Significance StatementSmall rivers and estuaries often carry pollutants, sediments, and larvae into the coastal ocean, where wave action in the surf zone can trap them near the shore. This process can play an important role in the flux of material into and out of the nearshore ecosystem and presents a potential risk to swimmers when materials are harmful. The present study uses a numerical model to investigate the fate of freshwater discharged from small rivers into the surf zone and the processes through which trapped riverine freshwater escapes from the surf zone. These results establish a basis for predicting the fate of river-borne materials from coastal rivers and understanding the exchange between the surf zone and the inner shelf. Additionally, this work provides a theoretical framework for predicting the residence time and concentration of river-borne material trapped in the surf zone. 

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 The diversity of the marine cyanobacteriumSynechococcuscan be broadly separated into clades, with clade II typically present in warm oligotrophic water, and clades I and IV found in cooler coastal water. We found amplicon sequence variants (ASVs) belonging to clade II in the nutrient‐replete waters of San Diego Bay (SDB). Using the 16S rRNA gene, 18S rRNA gene and internal transcribed spacer region sequencing, we analysed multiple locations in SDB monthly for over a year, with additional samples dating back to 2015.Synechococcuscommunity composition differed from the nearby coast into SDB in terms of dominant clade and ASVs. Specific clade II ASVs became relatively more abundant towards the back of the bay and showed seasonality, with higher relative abundance in the warm months. Select ASVs group phylogenetically and show similar seasonal and spatial distribution patterns, indicating these ASVs have adapted to SDB. Isolates matching clade II ASVs from SDB show pigment composition that is better adapted to the green light available in SDB, further supporting our findings. Other microbial taxa also show SDB enrichment, providing evidence that SDB is a chemostat‐like environment where circulation, temperature, light and other environmental conditions create a zone for microbial evolution and diversification. 

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.