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.