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Abstract Estuarine exchange flow regulates aspects of estuarine biogeochemical processes; however, other tracer‐specific factors can also play an important role. Here, we analyze realistic simulations from a coupled physical‐biological model to quantify volume‐integrated budgets of heat, total nitrogen (TN), and dissolved oxygen (DO) in the Salish Sea and its sub‐basins. Our goal is to evaluate the role of exchange flow in shaping tracer budgets, extending beyond the traditionally emphasized salt budget in estuaries. The three budgets reveal that exchange flow is a consistently important term with a clear annual cycle, but its relative role differs across tracers. For heat, exchange flow‐driven cooling is primarily offset by atmospheric heating, with the two reaching opposing seasonal extremes in summer. For TN, seasonal variability is dominated by exchange flow, whereas the annual mean is dominated by inputs from rivers and wastewater outfalls, and a loss due to benthic denitrification. The DO budget is the most complex: sinks from exchange flow export and respiration are balanced by sources from photosynthesis and air‐sea transfer. Across all three budgets, the sign of the inflow‐outflow tracer concentration differences determines whether exchange flow imports or exports tracers. These concentration differences, which are strongly influenced by coastal wind conditions, set the distinct seasonality of the exchange flow budget terms, while variations in the exchange flow volume transport play a minor role. Our budget quantification approach, based on archived model output, can be extended to other tracers such as carbon and other estuaries for long‐term budget studies. 

Abstract Estuaries in the northern California current system (NCCS) experience seasonally reversing wind stress, which is expected to impact the origin and properties of inflowing ocean water. Wind stress has been shown to affect the source of estuarine inflow by driving alongshelf currents. However, the effects of vertical transport by wind‐driven Ekman dynamics and other shelf and slope currents on inflow are yet to be explored. Variations in inflow to two NCCS estuarine systems, the Salish Sea and the Columbia River estuary, were studied using particle tracking in a hydrodynamic model. Particles were released in a grid extending two degrees of latitude north and south of each estuary every two weeks of 2017 and tracked for sixty days. Inflow was identified as particles that crossed the estuary mouths. Wind stress was compared with initial horizontal and vertical positions and physical properties of shelf inflow particles. Inflow to the Salish Sea came from Vancouver Island and Washington slope water upwelled through canyons during upwelling‐favorable wind stress, and from Washington slope water or Columbia River plume water during downwelling‐favorable wind stress. Inflow to the Columbia River estuary came from Washington shelf bottom water during upwelling‐favorable wind stress and Oregon shelf surface water during downwelling‐favorable wind stress. For both estuaries, upwelling‐favorable wind stress direction was significantly correlated with a denser and deeper shelf inflow source north of the estuary mouth. These results may help predict the source and properties of inflow to estuaries in other regions with known wind or shelf current patterns. 

Abstract The Salish Sea is a large, fjordal estuarine system opening onto the northeast Pacific Ocean. It develops a strong estuarine exchange flow that draws in nutrients from the ocean and flushes the system on timescales of several months. It is difficult to apply existing dynamical theories of estuarine circulation there because of the extreme bathymetric complexity. A realistic numerical model of the system was manipulated to have stronger and weaker tides to explore the sensitivity of the exchange flow to tides. This sensitivity was explored over two timescales: annual means and the spring‐neap. Two theories for the estuarine exchange flow are: (a) “gravitational circulation” where exchange is driven by the baroclinic pressure gradient due to along‐channel salinity variation, and (b) “tidal pumping” where tidal advection combined with flow separation forces the exchange. Past observations suggested gravitational circulation was of leading importance in the Salish Sea. We find here that the exchange flow increases with stronger tides, particularly in annual averages, suggesting it is controlled by tidal pumping. However, the landward salt transport due to the exchange flow decreases with stronger tides because greater mixing decreases the salinity difference between incoming and outgoing water. These results may be characteristic of estuarine systems that have rough topography and strong tides. 

Abstract The exchange between estuaries and the coastal ocean is a key dynamical driver impacting nutrient and phytoplankton concentrations and regulating estuarine residence time, hypoxia, and acidification. Estuarine exchange flows can be particularly challenging to monitor because many systems have strong vertical and lateral velocity shear and sharp gradients in water properties that vary over space and time, requiring high‐resolution measurements in order to accurately constrain the flux. The total exchange flow (TEF) method provides detailed information about the salinity structure of the exchange, but requires observations (or model resolution) that resolve the time and spatial co‐variability of salinity and currents. The goal of this analysis is to provide recommendations for measuring TEF with the most efficient spatial sampling resolution. Results from three realistic hydrodynamic models were investigated. These model domains included three estuary types: a bay (San Diego Bay), a salt‐wedge (Columbia River), and a fjord (Salish Sea). Model fields were sampled using three different mooring strategies, varying the number of mooring locations (lateral resolution) and sample depths (vertical resolution) with each method. The exchange volume transport was more sensitive than salinity to the sampling resolution. Most (>90%) of the exchange flow magnitude was captured by three to four moorings evenly distributed across the estuarine channel with a minimum threshold of 1–5 sample depths, which varied depending on the vertical stratification. These results can improve our ability to observe and monitor the exchange and transport of water masses efficiently with limited resources. 

Abstract. Particle tracking is widely utilized to study transport features in a range of physical, chemical, and biological processes in oceanography. In this study, a new offline particle-tracking package, Tracker v1.1, is introduced, and its performance is evaluated in comparison to an online Eulerian dye, one online particle-tracking software package, and three offline particle-tracking software packages in a small, high-resolution model domain and a large coarser model domain. It was found that both particle and dye approaches give similar results across different model resolutions and domains when they were tracking the same water mass, as indicated by similar mean advection pathways and spatial distributions of dye and particles. The flexibility of offline particle tracking and its similarity against online dye and online particle tracking make it a useful tool to complement existing ocean circulation models. The new Tracker was shown to be a reliable particle-tracking package to complement the Regional Ocean Modeling System (ROMS) with the advantages of platform independence and speed improvements, especially in large model domains achieved by the nearest-neighbor search algorithm. Lastly, trade-offs of computational efficiency, modifiability, and ease of use that can influence the choice of which package to use are explored. The main value of the present study is that the different particle and dye tracking codes were all run on the same model output or within the model that generated the output. This allows some measure of intercomparison between the different tracking schemes, and we conclude that all choices that make each tracking package unique do not necessarily lead to very different results.