Environmental DNA (eDNA) analysis is a technique for detecting organisms based on genetic material in environments such as air, water, or soil. Observed eDNA concentrations vary in space and time due to biological and environmental processes. Here we investigate variability in eDNA production and loss by sampling water adjacent to a managed population of non-native cetaceans on a near-hourly timescale for 48 hours. We used diverse sampling approaches and modeling methods to describe time variability in observed eDNA concentrations and then compare the magnitude of production and loss mechanisms. We parsed production and loss in a Bayesian process model, and compared biological and physical loss rates using a decay experiment and a physical transport-and-diffusion tracer model. We then evaluated eDNA concentrations along a transect away from the animal enclosure in light of model parameter estimates. We conclude that eDNA production is best conceptualized using a time-varying mixed-state model and biological losses are small relative to physical losses in the marine environment. Because physical loss is unsteady and nonlinear, tracer models are especially helpful tools to estimate it accurately.

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.