Urbanization subjects stream and groundwater to increased loads of organic nitrogen, nitrate, and ammonium. Therefore, studying nitrogen species at the urban stream-aquifer interface is important for water resource management. We report here results on water 18O/16O ratios and on nitrogen species in stream subsurface waters upstream and downstream of several combined sewer overflows (CSOs) in a rural area and peri-urban area, respectively. Water 18O/16O ratios were measured to trace the mixing of subsurface waters with stream channel water. Organic nitrogen (ON) and carbon (OC) slightly increased between rural and peri-urban environments in the cold season, but not in the warm season. The highest nitrate levels were observed in rural subsurface waters in the cold season. The lowest nitrate levels were found in peri-urban subsurface waters in the warm season; they corresponded to slow exchange of subsurface waters with channel water.