Environmental DNA (eDNA) is increasingly used for species detection and biodiversity monitoring in estuary and marine environments. The dynamic nature of these environments affects eDNA distribution relative to its source organisms, complicating the interpretation of eDNA observations and challenging the field sampling design. Here, an eDNA fate and transport model, built on an ocean model with Lagrangian particle tracking, provided a spatiotemporal estimate of the rapidly diluted eDNA shed by rare targets in an estuary environment before sampling. Based on the predicted particle densities, over 70% of the preselected stations detected the target eDNA. Despite potential variations in source strength and patchy distributions, the model explained approximately 40% of the observed variation in eDNA abundance; by comparison, eDNA concentration was uncorrelated with straight-line distance from the source or with a simplified oceanographic model. Our study revealed the extent of advective transport in shaping eDNA distribution and abundance and demonstrated the utility of ocean models and particle tracking in integrating marine eDNA observations with degradation, transport, and dilution processes; thus, it suggests broader applications to enhance understanding of eDNA signals and dispersal and optimize sampling strategies in other estuarine or marine environments.