Nutrient pollution from rivers, nonpoint source runoff, and nearly 100 wastewater discharges is a potential threat to the ecological health of Puget Sound with evidence of hypoxia in some basins. However, the relative contributions of loads entering Puget Sound from natural and anthropogenic sources, and the effects of exchange flow from the Pacific Ocean are not well understood. Development of a quantitative model of Puget Sound is thus presented to help improve our understanding of the annual biogeochemical cycles in this system using the unstructured grid Finite-Volume Coastal Ocean Model framework and the Integrated Compartment Model (CE-QUAL-ICM) water quality kinetics. Results based on 2006 data show that phytoplankton growth and die-off, succession between two species of algae, nutrient dynamics, and dissolved oxygen in Puget Sound are strongly tied to seasonal variation of temperature, solar radiation, and the annual exchange and flushing induced by upwelled Pacific Ocean waters. Concentrations in the mixed outflow surface layer occupying approximately 5–20 m of the upper water column show strong effects of eutrophication from natural and anthropogenic sources, spring and summer algae blooms, accompanied by depleted nutrients but high dissolved oxygen levels. The bottom layer reflects dissolved oxygen and nutrient concentrations of upwelled Pacific Ocean water modulated by mixing with biologically active surface outflow in the Strait of Juan de Fuca prior to entering Puget Sound over the Admiralty Inlet. The effect of reflux mixing at the Admiralty Inlet sill resulting in lower nutrient and higher dissolved oxygen levels in bottom waters of Puget Sound than the incoming upwelled Pacific Ocean water is reproduced. By late winter, with the reduction in algal activity, water column constituents of interest, were renewed and the system appeared to reset with cooler temperature, higher nutrient, and higher dissolved oxygen waters from the Pacific Ocean.

Given annual occurrences of hypoxia, harmful algal blooms, and evidence of coastal acidification, the potential impacts of climate change on water quality are of increasing concern in the U.S. Pacific Northwest estuaries such as the Salish Sea. While large‐scale global climate projections are well documented, our understanding of the nearshore estuarine‐scale response is not as well developed. In this study, the future response within the Salish Sea fjord‐like environment was examined using the Salish Sea Model driven by downscaled outputs from the National Center for Atmospheric Research climate model Community Earth System Model. We simulated a single projection of 95‐year change under the representative concentration pathway 8.5 greenhouse gas emissions scenario. Results indicate that higher temperatures, lower pH, and decreased dissolved oxygen levels in the upwelled shelf waters in the future would propagate into the Salish Sea. Results point to potential changes in average Salish Sea temperature (≈+1.51 °C), dissolved oxygen (≈−0.77 mg/L), and pH (acidification −0.18 units) in the Y2095 relative to historical Y2000. The algal biomass in the Salish Sea could increase by ≈23% with a potential species shift from diatoms toward dinoflagellates. The region of annually recurring hypoxia could increase from <1% today to ≈16% in the future. The results suggest that the future response in the Salish Sea is less severe relative to the change predicted near the continental shelf boundary. This resilience of the Salish Sea may be attributed to the existence of strong vertical circulation cells that provide mitigation and serve as a physical buffer, thus keeping waters cooler, more oxygenated, and less acidic.

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.

Increasing levels of nutrients, persistent hypoxia, harmful algal blooms, and increased frequency of fish kills are degrading the ecological health of the Salish Sea. An improved version of a diagnostic hydrodynamic and biogeochemical model (nutrients, phytoplankton, carbon, dissolved oxygen, and pH) of the Salish Sea has been developed with the ability to simulate characteristic circulation and water quality features. Sensitivity tests were conducted to assess the responsiveness of the system to land‐based (rivers and wastewater sources) nutrient loading. The influence of Fraser River on the magnitude of estuarine exchange with the Pacific Ocean and nearshore habitat was examined given that it contributes nearly half of the total freshwater discharged to the Salish Sea. A large region of hypoxia in Hood Canal that extends over 30–40 km during its peak was reproduced and attributed primarily to the existence of a two‐layer classic fjord‐type circulation and a nearly stagnant deep bottom layer that occupies nearly 60% of the water column. Nitrate mass in the euphotic zone from land‐based and oceanic sources is depleted to near‐zero limiting levels during summer. Under such conditions, the Salish Sea is responsive to changes in nutrient loads entering the euphotic zone directly. A hypothetical scenario involving the elimination of land‐based nutrient sources results in notable water‐quality improvement, featuring a reduction in algal biomass (≈5.4%), reduction in sediment oxygen demand (≈17.1%), and significant reduction in hypoxic area (≈39%) and exposure in area‐days to bottom layer hypoxia (≈62%) within the Salish Sea.

While ocean acidification was first investigated as a global phenomenon, coastal acidification has received significant attention in recent years, as its impacts have been felt by different socio-economic sectors (e.g., high mortality of shellfish larvae in aquaculture farms). As a region that connects land and ocean, the Salish Sea (consisting of Puget Sound and the Straits of Juan de Fuca and Georgia) receives inputs from many different sources (rivers, wastewater treatment plants, industrial waste treatment facilities, etc.), making these coastal waters vulnerable to acidification. Moreover, the lowering of pH in the Northeast Pacific Ocean also affects the Salish Sea, as more acidic waters get transported into the bottom waters of the straits and estuaries. Here, we use a numerical ocean model of the Salish Sea to improve our understanding of the carbonate system in Puget Sound; in particular, we studied the sensitivity of carbonate variables (e.g., dissolved inorganic carbon, total alkalinity, pH, saturation state of aragonite) to ocean and freshwater inputs. The model is an updated version of our FVCOM-ICM framework, with new carbonate-system and sediment modules. Sensitivity experiments altering concentrations at the open boundaries and freshwater sources indicate that not only ocean conditions entering the Strait of Juan de Fuca, but also the dilution of carbonate variables by freshwater sources, are key drivers of the carbonate system in Puget Sound.

Marine CO₂ removal (CDR) using enhanced-alkalinity seawater discharge was simulated in the estuarine waters of the Salish Sea, Washington, US. The high-alkalinity seawater would be generated using bipolar membrane electrodialysis technology to remove acid and the alkaline stream returned to the sea. Response of the receiving waters was evaluated using a shoreline resolving hydrodynamic model with biogeochemistry, and carbonate chemistry. Two sites, and two deployment scales, each with enhanced TA of 2997 mmol m⁻³ and a pH of 9 were simulated. The effects on air-sea CO₂ flux and pH in the near-field as well as over the larger estuary wide domain were assessed. The large-scale deployment (addition of 164 Mmoles TA yr⁻¹) in a small embayment (Sequim Bay, 12.5 km²) resulted in removal of 2066 T of CO₂ (45% of total simulated) at rate of 3756 mmol m⁻² yr⁻¹, higher than the 63 mmol m⁻² yr⁻¹ required globally to remove 1.0 GT CO₂ yr⁻¹. It also reduced acidity in the bay, ΔpH ≈ +0.1 pH units, an amount comparable to the historic impacts of anthropogenic acidification in the Salish Sea. The mixing and dilution of added TA with distance from the source results in reduced CDR rates such that comparable amount 2176 T CO₂ yr⁻¹ was removed over >1000 fold larger area of the rest of the model domain. There is the potential for more removal occurring beyond the region modeled. The CDR from reduction of outgassing between October and May accounts for as much as 90% of total CDR simulated. Of the total, only 375 T CO₂ yr⁻¹ (8%) was from the open shelf portion of the model domain. With shallow depths limiting vertical mixing, nearshore estuarine waters may provide a more rapid removal of CO₂ using alkalinity enhancement relative to deeper oceanic sites.