Soluble nutrient flux is increasingly implicated in the degradation of receiving water quality. With high-frequency sensors, river discharge along with nitrate and orthophosphate concentrations were collected over 2 years. We examined how storms (16 events) affected the dissolved nutrient flux in two watersheds with contrasting landcover—urban and agricultural. The adjacent watersheds, both < 7 km2, had very similar soil, slope, relief, and physiography. Wastewater is conveyed outside of the watersheds minimizing this nutrient source. Cumulative nitrate and orthophosphate fluxes in the agricultural watershed were substantially higher than the urban watershed. In both watersheds, a disproportionate amount of discharge, higher orthophosphate concentrations and flux occurred during the highest flow events—approximately 50–70% of flux occurring in the highest 5% of daily discharge. The nitrate flux was dampened compared to discharge during storm events. Baseflow accounted for 66% of the nitrate flux and had higher or comparable concentrations than storm events. The pattern of flux and concentration within storm events also differed for the two solutes. Nitrate exhibited positive hysteresis (higher concentrations on the rising limb of the hydrograph) and magnification of flux during the first flush of storm runoff. In contrast, orthophosphate concentrations were lower on the rising limb and flux during the first flush of storm runoff was dampened. In addition to targeting source reductions, orthophosphate flux may require runoff reducing strategies (i.e., enhanced infiltration) from large runoff events. First flush stormwater management practices combined with enhancement/protection of groundwater nitrate sinks (e.g., riparian wetlands) may help reduce nitrate fluxes.