Ephemeral streams are important pollutant conduits, but the mechanisms that control nutrient transport to these systems remain unclear. In the US Virgin Islands (USVI), where most streams flow ephemerally, a lack of continuous hydrologic and water quality data limits our understanding of streamflow behavior and its influence on water quality. We therefore assessed the impact of soil moisture and hydrometeorological conditions on nitrogen (N) concentrations within an ephemeral stream on St. Croix, USVI. Stream N concentrations were usually highest during initial flow events, after prolonged dryness, and declined thereafter. Nitrogen increased with shallow antecedent soil moisture and rainfall intensity and decreased with deep soil moisture and baseflow emergence, indicating it was predominantly exported to the stream via surface runoff, as opposed to subsurface leaching. Our results are the first of their kind for the USVI and could be used to improve water quality of freshwater and marine systems.