Transport of nitrogen and phosphorus from agricultural and urban landscapes to surface water bodies can cause adverse environmental impacts. The main objective of this long-term study was to quantify and compare contaminant transport in agricultural drainage water and urban stormwater runoff. We measured flow rate and contaminant concentration in stormwater runoff from Willmar, Minnesota, USA, and in drainage water from subsurface-drained fields with surface inlets, namely, Unfertilized and Fertilized Fields. Commercial fertilizer and turkey litter manure were applied to the Fertilized Field based on agronomic requirements. Results showed that the City Stormwater transported significantly higher loads per unit area of ammonium, total suspended solids (TSS), and total phosphorus (TP) than the Fertilized Field, but nitrate load was significantly lower. Nitrate load transport in drainage water from the Unfertilized Field was 58% of that from the Fertilized Field. Linear regression analysis indicated that a 1% increase in flow depth resulted in a 1.05% increase of TSS load from the City Stormwater, a 1.07% increase in nitrate load from the Fertilized Field, and a 1.11% increase in TP load from the Fertilized Field. This indicates an increase in concentration with a rise in flow depth, revealing that concentration variation was a significant factor influencing the dynamics of load transport. Further regression analysis showed the importance of targeting high flows to reduce contaminant transport. In conclusion, for watersheds similar to this one, management practices should be directed to load reduction of ammonium and TSS from urban areas, and nitrate from cropland while TP should be a target for both.