The exchange flow is widely recognized as a defining property of tidally averaged estuarine circulation. The persistent inflow of deep, salty water and outflow of shallow, somewhat fresher water is often many times greater in volume flux than all the rivers entering a system. As a result, the exchange flow controls residence times and biogeochemical gradients. Physically this circulation is a result of the density contrast between ocean and river water, combined with mixing and advection from tidal currents (Geyer & MacCready, 2014; MacCready & Geyer, 2010). The theory of estuarine exchange flow was developed and tested for shallow, straight coastal plain estuaries such as the Hudson (Hansen & Rattray, 1965; Ralston et al., 2008) but is less well-developed for more complex systems. In this paper we focus on the circulation of one of these complex systems-the Salish Sea, a large, interconnected system of very deep basins and shallow straits forced by Abstract A realistic numerical model is used to study the circulation and mixing of the Salish Sea, a large, complex estuarine system on the United States and Canadian west coast. The Salish Sea is biologically productive and supports many important fisheries but is threatened by recurrent hypoxia and ocean acidification, so a clear understanding of its circulation patterns and residence times is of value. The estuarine exchange flow is quantified at 39 sections over 3 years (2017-2019) using the Total Exchange Flow method. Vertical mixing in the 37 segments between sections is quantified as opposing vertical transports: the efflux and reflux. Efflux refers to the rate at which deep, landward-flowing water is mixed up to become part of the shallow, seaward-flowing layer. Similarly, reflux refers to the rate at which upper layer water is mixed down to form part of the landward inflow. These horizontal and vertical transports are used to create a box model to explore residence times in a number of different sub-volumes, seasons, and years. Residence times from the box model are generally found to be longer than those based on simpler calculations of flushing time. The longer residence times are partly due to reflux, and partly due to incomplete tracer homogenization in sub-volumes. The methods presented here are broadly applicable to other estuaries. Plain Language Summary The Salish Sea is a large estuarine system that includes the cities of Vancouver on the Strait of Georgia and Seattle on Puget Sound. Despite the many rivers flowing into the Salish Sea, the water in the system is mostly ocean water, and there is rapid exchange with the ocean. This exchange is important because it brings in most of the nutrients that feed the ecosystem, and it flushes the system relatively rapidly, leading to generally good water quality. Nonetheless, there are places and times in the Salish Sea that experience problems like hypoxia and fish kills. The goal of this work is to clearly describe the patterns of circulation and mixing throughout the Salish Sea so that we may understand th...

Ocean acidification poses serious threats to coastal ecosystem services, yet few empirical studies have investigated how local ecological processes may modulate global changes of pH from rising atmospheric CO2. We quantified patterns of pH variability as a function of atmospheric CO2 and local physical and biological processes at 83 sites over 25 years in the Salish Sea and two NE Pacific estuaries. Mean seawater pH decreased significantly at −0.009 ± 0.0005 pH yr−1 (0.22 pH over 25 years), with spatially variable rates ranging up to 10 times greater than atmospheric CO2-driven ocean acidification. Dissolved oxygen saturation (%DO) decreased by −0.24 ± 0.036% yr−1, with site-specific trends similar to pH. Mean pH shifted from <7.6 in winter to >8.0 in summer concomitant to the seasonal shift from heterotrophy (%DO < 100) to autotrophy (%DO > 100) and dramatic shifts in aragonite saturation state critical to shell-forming organisms (probability of undersaturation was >80% in winter, but <20% in summer). %DO overwhelmed the influence of atmospheric CO2, temperature and salinity on pH across scales. Collectively, these observations provide evidence that local ecosystem processes modulate ocean acidification, and support the adoption of an ecosystem perspective to ocean acidification and multiple stressors in productive aquatic habitats.

Abstract. Fingerprinting ocean acidification (OA) in US West Coast waters is extremely challenging due to the large magnitude of natural carbonate chemistry variations common to these regions. Additionally, quantifying a change requires information about the initial conditions, which is not readily available in most coastal systems. In an effort to address this issue, we have collated high-quality publicly available data to characterize the modern seasonal carbonate chemistry variability in marine surface waters of the US Pacific Northwest. Underway ship data from version 4 of the Surface Ocean CO2 Atlas, discrete observations from various sampling platforms, and sustained measurements from regional moorings were incorporated to provide  ∼  100 000 inorganic carbon observations from which modern seasonal cycles were estimated. Underway ship and discrete observations were merged and gridded to a 0.1°  ×  0.1° scale. Eight unique regions were identified and seasonal cycles from grid cells within each region were averaged. Data from nine surface moorings were also compiled and used to develop robust estimates of mean seasonal cycles for comparison with the eight regions. This manuscript describes our methodology and the resulting mean seasonal cycles for multiple OA metrics in an effort to provide a large-scale environmental context for ongoing research, adaptation, and management efforts throughout the US Pacific Northwest. Major findings include the identification of unique chemical characteristics across the study domain. There is a clear increase in the ratio of dissolved inorganic carbon (DIC) to total alkalinity (TA) and in the seasonal cycle amplitude of carbonate system parameters when moving from the open ocean North Pacific into the Salish Sea. Due to the logarithmic nature of the pH scale (pH  =  −log10[H+], where [H+] is the hydrogen ion concentration), lower annual mean pH values (associated with elevated DIC  :  TA ratios) coupled with larger magnitude seasonal pH cycles results in seasonal [H+] ranges that are  ∼  27 times larger in Hood Canal than in the neighboring North Pacific open ocean. Organisms living in the Salish Sea are thus exposed to much larger seasonal acidity changes than those living in nearby open ocean waters. Additionally, our findings suggest that lower buffering capacities in the Salish Sea make these waters less efficient at absorbing anthropogenic carbon than open ocean waters at the same latitude.All data used in this analysis are publically available at the following websites: Surface Ocean CO2 Atlas version 4 coastal data, https://doi.pangaea.de/10.1594/PANGAEA.866856 (Bakker et al., 2016a);National Oceanic and Atmospheric Administration (NOAA) West Coast Ocean Acidification cruise data, https://doi.org/10.3334/CDIAC/otg.CLIVAR_NACP_West_Coast_Cruise_2007 (Feely and Sabine, 2013); https://doi.org/10.7289/V5JQ0XZ1 (Feely et al., 2015b); https://data.nodc.noaa.gov/cgi-bin/iso?id=gov.noaa.nodc:0157445 (Feely et al., 2016a); https://doi.org/10.7289/V5C53HXP (Feely et al., 2015a);University of Washington (UW) and Washington Ocean Acidification Center cruise data, https://doi.org/10.5281/zenodo.1184657 (Fassbender et al., 2018);Washington State Department of Ecology seaplane data, https://doi.org/10.5281/zenodo.1184657 (Fassbender et al., 2018);NOAA Moored Autonomous pCO2 (MAPCO2) buoy data, https://doi.org/10.3334/CDIAC/OTG.TSM_LAPUSH_125W_48N (Sutton et al., 2012); https://doi.org/10.3334/CDIAC/OTG.TSM_WA_125W_47N (Sutton et al., 2013); https://doi.org/10.3334/CDIAC/OTG.TSM_DABOB_122W_478N (Sutton et al., 2014a); https://doi.org/10.3334/CDIAC/OTG.TSM_TWANOH_123W_47N (Sutton et al., 2016a);UW Oceanic Remote Chemical/Optical Analyzer buoy data, https://doi.org/10.5281/zenodo.1184657 (Fassbender et al., 2018);NOAA Pacific Coast Ocean Observing System cruise data, https://doi.org/10.5281/zenodo.1184657 (Fassbender et al., 2018).

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Effects and impacts of the Northeast Pacific marine heatwave of 2014–2016 on the inner coastal estuarine waters of the Salish Sea were examined using a combination of monitoring data and an established three-dimensional hydrodynamic and biogeochemical model of the region. The anomalous high temperatures reached the U.S. Pacific Northwest continental shelf toward the end of 2014 and primarily entered the Salish Sea waters through an existing strong estuarine exchange. Elevated temperatures up to + 2.3°C were observed at the monitoring stations throughout 2015 and 2016 relative to 2013 before dissipating in 2017. The hydrodynamic and biogeochemical responses to this circulating high-temperature event were examined using the Salish Sea Model over a 5-year window from 2013 to 2017. Responses of conventional water-quality indicator variables, such as temperature and salinity, nutrients and phytoplankton, zooplankton, dissolved oxygen, and pH, were evaluated relative to a baseline without the marine heatwave forcing. The simulation results relative to 2014 show an increase in biological activity (+14%, and 6% Δ phytoplankton biomass, respectively) during the peak heatwave year 2015 and 2016 propagating toward higher zooplankton biomass (+14%, +18% Δ mesozooplankton biomass). However, sensitivity tests show that this increase was a direct result of higher freshwater and associated nutrient loads accompanied by stronger estuarine exchange with the Pacific Ocean rather than warming due to the heatwave. Strong vertical circulation and mixing provided mitigation with only ≈+0.6°C domain-wide annual average temperature increase within Salish Sea, and served as a physical buffer to keep waters cooler relative to the continental shelf during the marine heatwave.