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In April and May of 2020, a large phytoplankton bloom composed primarily of the dinoflagellate Lingulodinium polyedra reached historic levels in geographic expanse, duration, and density along the coast of southern California, United States, and Baja California Norte, Mexico. Here, we report the water quality parameters of dissolved oxygen and pH over the course of the red tide, as measured by multiple sensors deployed in various locations along San Diego County, and document the extent of mass organism mortality using field surveys and community science observations. We found that dissolved oxygen and pH corresponded with bloom dynamics, with extreme hypoxic and hyperoxic conditions occurring at multiple locations along the coast, most notably within select estuaries where dissolved oxygen reached 0 mg L−1 and hypoxia occurred for up to 254 consecutive hours, as well as along the inner shelf of the open coast where dissolved oxygen dropped as low as 0.05 mg L−1. Similarly, pH ranged widely (6.90–8.79) across the bloom over both space and time, largely corresponding with dissolved oxygen level. Extreme changes in dissolved oxygen and pH, in addition to changes to other water parameters that affect organismal health, ultimately led to documented mortalities of thousands of demersal and benthic fishes and invertebrates (primarily within estuarine and inner-shelf environments), and long-term surveys within one lagoon showed protracted changes to benthic infaunal density and species composition. In addition to field observations, we also quantified water quality parameters and organism mortalities from four local aquarium facilities, with varying levels of filtration and artificial oxygenation, and documented the morphological changes in the gills of captive-held Pacific sardine in response to the red tide. We show that multiple factors contributed to organismal stress, with hypoxia likely being the most widespread, but not the only, cause of mortality.

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.

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

The popular beaches of the San Diego-Tijuana (US/MX) border region are often impacted by untreated wastewater sourced from Mexico-via the Tijuana River Estuary (TJRE) and San Antonio de los Buenos outfall at the Pt. Bandera (SAB/PTB) shoreline, leading to impacted beaches and human illness. The US-Mexico-Canada trade agreement will fund border infrastructure projects reducing untreated wastewater discharges. However, estimating project benefits such as reduced human illness and beach impacts is challenging. We develop a coupled hydrodynamic, norovirus (NoV) pathogen, and swimmer illness risk model with the wastewater sources for the year 2017. The model is used to evaluate the reduction in human illness and beach impacts under baseline conditions and three infrastructure diversion scenarios which (Scenario A) reduce SAB/PTB discharges and moderately reduce TJRE inflows or (Scenarios B, C) strongly reduce TJRE in inflows only. The model estimates shoreline untreated wastewater and NoV concentrations, and the number of NoV ill swimmers at Imperial Beach CA. In the Baseline, the percentage of swimmers becoming ill is 3.8% over 2017, increasing to 4.5% during the tourist season (Memorial to Labor Day) due to south-swell driven SAB/PTB plumes. Overall, Scenario A provides the largest reduction in ill swimmers and beach impacts for the tourist season and full year. The 2017 tourist season TJRE inflows were not representative of those in 2020, yet, Scenario A likely still provides the greatest benefit in other years. This methodology can be applied to other coastal regions with wastewater inputs.

AbstractHere, we explore the kinematics and dynamics of coastal density fronts (within 10 km from shore and

Each year, over one hundred million people become ill and tens of thousands die from exposure to viruses and bacteria from sewage transported to the ocean by rivers, estuaries, stormwater, and other coastal discharges. Water activities and seafood consumption have been emphasized as the major exposure pathways to coastal water pollution. In contrast, relatively little is known about the potential for airborne exposure to pollutants and pathogens from contaminated seawater. The Cross Surfzone/Inner-shelf Dye Exchange (CSIDE) study was a large-scale experiment designed to investigate the transport pathways of water pollution along the coast by releasing dye into the surfzone in Imperial Beach, CA. Additionally, we leveraged this ocean-focused study to investigate potential airborne transmission of coastal water pollution by collecting complementary air samples along the coast and inland. Aerial measurements tracked sea surface dye concentrations along 5+ km of coast at 2 m × 2 m resolution. Dye was detected in the air over land for the first 2 days during two of the three dye releases, as far as 668 m inland and 720 m downwind of the ocean. These coordinated water/air measurements, comparing dye concentrations in the air and upwind source waters, provide insights into the factors that lead to the water-to-air transfer of pollutants. These findings show that coastal water pollution can reach people through an airborne pathway and this needs to be taken into account when assessing the full impact of coastal ocean pollution on public health. This study sets the stage for further studies to determine the details and importance of airborne exposure to sewage-based pathogens and toxins in order to fully assess the impact of coastal pollution on public health.

AbstractTransport of shoreline-released tracer from the surfzone across the shelf can be affected by a variety of physical processes from wind-driven to submesoscale, with implications for shoreline contaminant dilution and larval dispersion. Here, a high-resolution wave–current coupled model that resolves the surfzone and receives realistic oceanic and atmospheric forcing is used to simulate dye representing shoreline-released untreated wastewater in the San Diego–Tijuana region. Surfzone and shelf alongshore dye transports are primarily driven by obliquely incident wave breaking and alongshore pressure gradients, respectively. At the midshelf to outer-shelf (MS–OS) boundary (25-m depth), defined as a mean streamline, along-boundary density gradients are persistent, dye is surface enhanced and time and alongshelf patchy. Using baroclinic and along-boundary perturbation dye transports, two cross-shore dye exchange velocities are estimated and related to physical processes. Barotropic and baroclinic tides cannot explain the modeled cross-shore transport. The baroclinic exchange velocity is consistent with the wind-driven Ekman transport. The perturbation exchange velocity is elevated for alongshore dye and cross-shore velocity length scales < 1 km (within the submesoscale) and stronger alongshore density gradient ∂ρ/∂y variability, indicating that alongfront geostrophic flows induce offshore transport. This elevated ∂ρ/∂y is linked to convergent northward surface along-shelf currents (likely due to regional bathymetry), suggesting deformation frontogenesis. Both surfzone and shelf processes influence offshore transport of shoreline-released tracers with key parameters of surfzone and shelf alongcoast currents and alongshelf winds.

The 2015–2016 El Niño provided insight into how low-inflow estuaries might respond to future climate regimes, including high sea levels and more intense waves. High waves and water levels coupled with low rainfall along the Southern California coastline provided the opportunity to examine how extreme ocean forcing impacts estuaries independently from fluvial events. From November 2015 to April 2016, water levels were measured in 13 Southern California estuaries, including both intermittently closed and perennially open estuaries with varying watershed size, urban development, and management practices. Elevated ocean water levels caused raised water levels and prolonged inundation in all of the estuaries studied. Water levels inside perennially open estuaries mirrored ocean water levels, while those inside intermittently closed estuaries (ICEs) exhibited enhanced higher-high water levels during large waves, and tides were truncated at low tides due to a wave-built sand sill at the mouth, resulting in elevated detided water levels. ICEs closed when sufficient wave-driven sand accretion formed a barrier berm across the mouth separating the estuary from the ocean, the height of which can be estimated using estuarine lower-low water levels. During the 2015–2016 El Niño, a greater number of Southern California ICEs closed than during a typical year and ICEs that close annually experienced longer than normal closures. Overall, sill accretion and wave exposure were important contributing factors to individual estuarine response to ocean conditions. Understanding how estuaries respond to increased sea levels and waves and the factors that influence closures will help managers develop appropriate adaptation strategies.

Abstract: An inner-shelf (IS) dye plume that formed following a 3.84-h early morning surfzone (SZ) dye release off of Imperial Beach, California, is analyzed with in situ and aerial remotely sensed observations. Midmorning, 5 h after release start, the IS plume extended 800 m offshore (or ≈8Lsz, where Lsz is the surfzone width) and was surface intensified. Over the next ≈2 h, the IS plume deformed (narrowed) cross-shore with the offshore front progressing onshore at ≈5 cm s−1, deepened by up to 3 m, and elongated alongshore at ≈4.5 cm s−1 km−1 (at ≈2.5Lsz). Coincident with IS plume deformation and deepening, IS isotherms also deepened, with relatively stable IS plume joint dye and temperature statistics. Offshore tracer transport and subsequent IS plume deformation and deepening likely resulted from two phases of the diurnal internal tide (DIT). During and after deformation, the IS plume did not reenter the warm surfzone, which potentially acted as a thermal barrier. High-frequency internal waves (HF IWs) propagated through the IS plume at ≈9 cm s−1 and dissipated onshore of 4Lsz. Surface HF IW signal was elevated in the plume elongation region, suggesting a linkage between plume elongation and either the DIT or HF IW. This IS plume evolution differs from previous SZ tracer releases, highlighting the effects of release timing relative to the solar cycle or the internal tide.

Ocean acidification threatens many marine organisms, especially marine calcifiers. The only global-scale solution to ocean acidification remains rapid reduction in CO2 emissions. Nevertheless, interest in localized mitigation strategies has grown rapidly because of the recognized threat ocean acidification imposes on natural communities, including ones important to humans. Protection of seagrass meadows has been considered as a possible approach for localized mitigation of ocean acidification due to their large standing stocks of organic carbon and high productivity. Yet much work remains to constrain the magnitudes and timescales of potential buffering effects from seagrasses. We developed a biogeochemical box model to better understand the potential for a temperate seagrass meadow to locally mitigate the effects of ocean acidification. Then we parameterized the model using data from Tomales Bay, an inlet on the coast of California, USA which supports a major oyster farming industry. We conducted a series of month-long model simulations to characterize processes that occur during summer and winter. We found that average pH in the seagrass meadows was typically within 0.04 units of the pH of the primary source waters into the meadow, although we did find occasional periods (hours) when seagrass metabolism may modify the pH by up to ±0.2 units. Tidal phasing relative to the diel cycle modulates localized pH buffering within the seagrass meadow such that maximum buffering occurs during periods of the year with midday low tides. Our model results suggest that seagrass metabolism in Tomales Bay would not provide long-term ocean acidification mitigation. However, we emphasize that our model results may not hold in meadows where assumptions about depth-averaged net production and seawater residence time within the seagrass meadow differ from our model assumptions. Our modeling approach provides a framework that is easily adaptable to other seagrass meadows in order to evaluate the extent of their individual buffering capacities. Regardless of their ability to buffer ocean acidification, seagrass meadows maintain many critically important ecosystem goods and services that will be increasingly important as humans increasingly affect coastal ecosystems.

AbstractA method is presented for calculating a complete, numerically closed, mechanical energy budget in a realistic simulation of circulation in a coastal–estuarine domain. The budget is formulated in terms of the “local” available potential energy (APE; Holliday and McIntyre 1981). The APE may be split up into two parts based on whether a water parcel has been displaced up or down relative to its rest depth. This decomposition clearly shows the different APE signatures of coastal upwelling (particles displaced up by wind) and the estuary (particles displaced down by mixing). Because the definition of APE is local in almost the same sense that kinetic energy is, this study may form meaningful integrals of reservoir and budget terms even over regions that have open boundaries. However, the choice of volume to use for calculation of the rest state is not unique and may influence the results. Complete volume-integrated energy budgets over shelf and estuary volumes in a realistic model of the northeast Pacific and Salish Sea give a new way to quantify the state of these systems and the physical forces that influence that state. On the continental shelf, upwelling may be quantified using APE, which is found to have order-one seasonal variation with an increase due to winds and decrease due to mixing. In the Salish Sea estuarine system, the APE has much less seasonal variation, and the magnitude of the most important forcing terms would take over 7 months to fully drain this energy.

The Pacific Northwest (PNW) shelf is the most biologically productive region in the California Current System. A coupled physical-biogeochemical model is used to investigate the influence of freshwater inputs on the productivity of PNW shelf waters using realistic hindcasts and model experiments that omit outflow from the Columbia River and Strait of Juan de Fuca (outlet for the Salish Sea estuary). Outflow from the Strait represents a critical source of nitrogen to the PNW shelf-accounting for almost half of the primary productivity on the Vancouver Island shelf, a third of productivity on the Washington shelf, and a fifth of productivity on the Oregon shelf during the upwelling season. The Columbia River has regional effects on the redistribution of phytoplankton, but does not affect PNW productivity as strongly as does the Salish Sea. A regional nutrient budget shows that nitrogen exiting the Strait is almost entirely (98%) of ocean-origin - upwelled into the Strait at depth, mixed into surface waters by tidal mixing, and returned to the coastal ocean. From the standpoint of nitrogen availability in the coastal euphotic zone, the estuarine circulation driven by freshwater inputs to the Salish Sea is more important than the supply of terrigenous nitrogen by rivers. Nitrogen-rich surface waters exiting the Strait follow two primary pathways - to the northwest in the Vancouver Island Coastal Current and southward toward the Washington and Oregon shelves. Nitrogen flux from the Juan de Fuca Strait and Eddy Region to these shelves is comparable to flux from local wind-driven upwelling.

Residual (subtidal) circulation profiles in estuaries with a large tidal amplitude-to-depth ratio often are quite complex and do not resemble the traditional estuarine gravitational circulation profile. This paper describes how a depth-normalized s-coordinate system allows for a more physical interpretation of residual circulation profiles than does a fixed vertical coordinate system in an estuary with a tidal amplitude comparable to the mean depth. Depth-normalized coordinates permit the approximation of Lagrangian residuals, performance of empirical orthogonal function (EOF) analysis, estimation of terms in the along-stream momentum equations throughout depth, and computation of a tidally averaged momentum balance. The residual mass transport velocity has an enhanced two-layer exchange flow relative to an Eulerian mean because of the Stokes wave transport velocity directed upstream at all depths. While the observed s-coordinate profiles resemble gravitational circulation, and pressure and friction are the dominant terms in the tidally varying and tidally averaged momentum equations, the two-layer shear velocity from an EOF analysis does not correlate with the along-stream density gradient. To directly compare to theoretical profiles, an extension of a pressure-friction balance in s coordinates is solved. While the barotropic riverine residual matches theory, the mean longitudinal density gradient and mean vertical mixing cannot explain the magnitude of the observed two-layer shear residual. In addition, residual shear circulation in this system is strongly driven by asymmetries during the tidal cycle, particularly straining and advection of the salinity field, creating intratidal variation in stratification, vertical mixing, and shear. © 2014 American Meteorological Society.

Infragravity (IG) waves are low-frequency water waves, which can propagate into harbors and estuaries, affecting currents and sediment transport processes. Understanding and predicting IG oscillations inside harbors and estuaries is critical to coastal management and estimating future resilience to climate change impacts. High-resolution water level and flow velocity observations collected within Seal Beach Wildlife Refuge in Southern California are analyzed for IG energy related to atmospheric parameters, water levels, and offshore wave conditions. A proof of concept approach for predicting infragravity oscillations within an estuary using machine learning (ML) is presented. [ABSTRACT FROM AUTHOR]

Agua Hedionda Lagoon (AHL), a tidal estuary located on the southern California coast, supports a diverse ecosystem while serving numerous recreation activities, a marine fish hatchery, a shellfish hatchery, and the largest desalination plant in the western hemisphere. In this work, a 1-year time series of carbon dioxide data is used to establish baseline average dissolved inorganic carbon conditions in AHL. Based on a mass balance model of the outer basin of the lagoon, we propose that AHL is a source of inorganic carbon to the adjacent ocean, through advective export, at a rate of 5.9 × 106 mol C year−1, and a source of CO2 to the atmosphere of 0.21 × 106 mol C year−1 (1 mol C m−2 year−1), implying a net heterotrophic system on the order of 6.0 × 106 mol C year−1 (30 mol C m−2 year−1). Although variable with a range throughout the year of 80% about the mean, the ecosystem remained persistently heterotrophic, reaching peak rates during the summer season. Using results from the mass balance, the annual cycle of selected properties of the aqueous CO2 system (pH, pCO2, and CaCO3 saturation state) were mathematically decomposed in order to examine the relative contribution of drivers including advection, ecosystem metabolism, and temperature that act to balance their observed annual cycle. Important findings of this study include the identification of advection as a prime driver of biogeochemical variability and the establishment of a data-based estimate of mean flushing time for AHL. [ABSTRACT FROM AUTHOR]

This manuscript presents several improvements to methods for despiking and measuring turbulent dissipation values with acoustic Doppler velocimeters (ADVs). This includes an improved inertial subrange fitting algorithm relevant for all experimental conditions as well as other modifications designed to address failures of existing methods in the presence of large infragravity (IG) frequency bores and other intermittent, nonlinear processes. We provide a modified despiking algorithm, wavenumber spectrum calculation algorithm, and inertial subrange fitting algorithm that together produce reliable dissipation measurements in the presence of IG frequency bores, representing turbulence over a 30 min interval. We use a semi-idealized model to show that our spectrum calculation approach works substantially better than existing wave correction equations that rely on Gaussian-based velocity distributions. We also find that our inertial subrange fitting algorithm provides more robust results than existing approaches that rely on identifying a single best fit and that this improvement is independent of environmental conditions. Finally, we perform a detailed error analysis to assist in future use of these algorithms and identify areas that need careful consideration. This error analysis uses error distribution widths to find, with 95% confidence, an average systematic uncertainty of ±15.2% and statistical uncertainty of ±7.8% for our final dissipation measurements. In addition, we find that small changes to ADV despiking approaches can lead to large uncertainties in turbulent dissipation and that further work is needed to ensure more reliable despiking algorithms. Significance Statement: Turbulent mixing is a process where the random movement of water can lead to water with different properties irreversibly mixing. This process is important to understand in estuaries because the extent of mixing of freshwater and saltwater inside an estuary alters its overall circulation and thus affects ecosystem health and the distribution of pollution or larvae in an estuary, among other things. Existing approaches to measuring turbulent dissipation, an important parameter for evaluating turbulent mixing, make assumptions that fail in the presence of certain processes, such as long-period, breaking waves in shallow estuaries. We evaluate and improve data analysis techniques to account for such processes and accurately measure turbulent dissipation in shallow estuaries. Some of our improvements are also relevant to a broad array of coastal and oceanic conditions. [ABSTRACT FROM AUTHOR]

Transport of shoreline-released tracer from the surfzone across the shelf can be affected by a variety of physical processes from wind-driven to submesoscale, with implications for shoreline contaminant dilution and larval dispersion. Here, a high-resolution wave-current coupled model that resolves the surfzone and receives realistic oceanic and atmospheric forcing is used to simulate dye representing shoreline-released untreated wastewater in the San Diego-Tijuana region. Surfzone and shelf alongshore dye transports are primarily driven by obliquely incident wave breaking and alongshore pressure gradients, respectively. At the midshelf to outer-shelf (MS-OS) boundary (25-m depth), defined as a mean streamline, along-boundary density gradients are persistent, dye is surface enhanced and time and alongshelf patchy. Using baroclinic and along-boundary perturbation dye transports, two cross-shore dye exchange velocities are estimated and related to physical processes. Barotropic and baroclinic tides cannot explain the modeled cross-shore transport. The baroclinic exchange velocity is consistent with the wind-driven Ekman transport. The perturbation exchange velocity is elevated for alongshore dye and cross-shore velocity length scales, 1 km (within the submesoscale) and stronger alongshore density gradient ...r/...y variability, indicating that alongfront geostrophic flows induce offshore transport. This elevated ...r/...y is linked to convergent northward surface along-shelf currents (likely due to regional bathymetry), suggesting deformation frontogenesis. Both surfzone and shelf processes influence offshore transport of shoreline-released tracers with key parameters of surfzone and shelf alongcoast currents and alongshelf winds. [ABSTRACT FROM AUTHOR]