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.