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Eutrophication of urban surface waters from excess nitrogen (N) and phosphorus (P) inputs remains a major issue in water quality management. Although much research has focused on understanding loading of nutrients from storm events, there has been little research to understand the contribution of baseflow, the water moving through storm drains between rainfall events. We investigated the relative contributions of baseflow versus stormflow for loading of water and nutrients (various forms of N and P) by the storm drain network in six urban sub-watersheds in St. Paul, MN, USA. Across sites, baseflow made substantial contributions to warm season (May–October) water yields (27–66� % across sites), total N yields (31–68� %), and total P yields (7–32� %). These results show that while P was predominantly delivered by stormflow, N loading was similar between baseflow and stormflow. We found that baseflow was dominated by groundwater inputs, likely caused by interception of shallow groundwater by storm drains, but also that variability in N and P among sites was related in part to the connectivity of the storm drains to upstream lakes and wetlands in some watersheds. The substantial loading by groundwater-dominated baseflow, especially for N, implies that N management may require a broader focus on N source reduction, perhaps through improved land management, in order to prevent contamination of shallow groundwater via infiltration.