Estuarine exchange flow regulates all aspects of estuarine biogeochemical processes, especially residence time. However, the motivation for residence time studies is biogeochemistry, and this can be influenced by much more than the exchange flow, depending on the tracer in question. In this study, we analyzed realistic simulations from a coupled physical-biological model to quantify the volume-integrated budgets of heat, total nitrogen (TN), and dissolved oxygen (DO) in the Salish Sea and its inner basins. The goal was to determine the relative importance of the exchange flow compared to other processes. The three budgets reveal that the exchange flow always plays a leading role, with a clear annual cycle, but is balanced by a different collection of other terms in each case. The heat budget is primarily a balance between the exchange flow cooling and atmospheric heating, with both terms peaking in the summer. The time variation of TN is dominated by the exchange flow, but the annual average is dominated by sources from rivers and wastewater and a sink from benthic denitrification. The DO budget has the most complex set of influences, with sinks due to the exchange flow and respiration, balanced by sources from photosynthesis and air-sea transfer. In all three budgets the difference between the inflow and outflow tracer concentrations, greatly affected by coastal wind conditions, determines the distinct seasonality of the exchange flow budget terms. In contrast, variation of the exchange flow volume transport plays a minor role.

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 have 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.

Estuaries in the northern California current system (NCCS) experience seasonally reversing wind stress, which is expected to impact the origin and properties of shelf water which enters NCCS estuaries (’shelf inflow’). Wind stress has been shown to affect the source of shelf inflow by driving alongshelf currents. However, the effects of wind-driven Ekman dynamics and shelf currents from larger-scale forcing on shelf inflow have yet to be explored. Variations in shelf inflow to the Salish Sea and the Columbia River estuary, two large NCCS estuarine systems, were studied using a realistic hydrodynamic model. The paths and source of shelf water were identified using particles released on the shelf. Particles were released every two weeks of 2017 and tracked for sixty days. Shelf inflow was identified as particles that crossed the estuary mouths. Mean wind stress during each release was compared with initial horizontal and vertical positions and physical properties of shelf inflow particles. For both the Salish Sea and the Columbia River estuary, upwelling-favorable wind stress was correlated with a shelf inflow source north of the estuary mouth. Depth was not correlated with wind stress for either estuary, but relative depth (depth scaled by isobath) increased during upwelling-favorable winds for both. Properties of inflow changed from cold and fresh during upwelling to warm and salty during downwelling, reflecting seasonal changes in NCCS shelf waters. These results may be extended to predict the source and properties of shelf inflow to estuaries in other regions with known wind or shelf current patterns.

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 three 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 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.

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.