Managing excess nutrients remains a major obstacle to improving ecosystem service benefits of urban waters. To inform more ecologically based landscape nutrient management, we compared watershed inputs, outputs, and retention for nitrogen (N) and phosphorus (P) in seven subwatersheds of the Mississippi River in St. Paul, Minnesota. Lawn fertilizer and pet waste dominated N and P inputs, respectively, underscoring the importance of household actions in influencing urban watershed nutrient budgets. Watersheds retained only 22% of net P inputs versus 80% of net N inputs (watershed area-weighted averages, where net inputs equal inputs minus biomass removal) despite relatively low P inputs. In contrast to many nonurban watersheds that exhibit high P retention, these urban watersheds have high street density that enhanced transport of P-rich materials from landscapes to stormwater. High P exports in storm drainage networks and yard waste resulted in net P losses in some watersheds. Comparisons of the N/P stoichiometry of net inputs versus storm drain exports implicated denitrification or leaching to groundwater as a likely fate for retained N. Thus, these urban watersheds exported high quantities of N and P, but via contrasting pathways: P was exported primarily via stormwater runoff, contributing to surface water degradation, whereas N losses additionally contribute to groundwater pollution. Consequently, N management and P management require different strategies, with N management focusing on reducing watershed inputs and P management also focusing on reducing P movement from vegetated landscapes to streets and storm drains.