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.