Growing urban environments stress hydrologic systems and impact downstream water quality. We examined a third-order catchment that transitions from an undisturbed mountain environment into urban Salt Lake City, Utah. We performed synoptic surveys during a range of seasonal baseflow conditions and utilized multiple lines of evidence to identify mechanisms by which urbanization impacts water quality. Surface water chemistry did not change appreciably until several kilometers into the urban environment, where concentrations of solutes such as chloride and nitrate increase quickly in a gaining reach. Groundwater springs discharging in this gaining system demonstrate the role of contaminated baseflow from an aquifer in driving stream chemistry. Hydrometric and hydrochemical observations were used to estimate that the aquifer contains approximately 18% water sourced from the urban area. The carbon and nitrogen dynamics indicated the urban aquifer also serves as a biogeochemical reactor. The evidence of surface water-groundwater exchange on a spatial scale of kilometers and time scale of months to years suggests a need to evolve the hydrologic model of anthropogenic impacts to urban water quality to include exchange with the subsurface. This has implications on the space and time scales of water quality mitigation efforts.