Nonpoint source nitrogen (N) pollution is a leading contributor to U.S. water quality impairments. We combined watershed N mass balances and stable isotopes to investigate fate and transport of nonpoint N in forest, agricultural, and urbanized watersheds at the Baltimore Long-Term Ecological Research site. Annual N retention was 55%, 68%, and 82% for agricultural, suburban, and forest watersheds, respectively. Analysis of δ¹⁵N-NO₃^–, and δ¹⁸O-NO₃^– indicated wastewater was an important nitrate source in urbanized streams during baseflow. Negative correlations between δ¹⁵N-NO₃^– and δ¹⁸O-NO₃^– in urban watersheds indicated mixing between atmospheric deposition and wastewater, and N source contributions changed with storm magnitude (atmospheric sources contributed ∼50% at peak storm N loads). Positive correlations between δ¹⁵N-NO₃^– and δ¹⁸O-NO₃^– in watersheds suggested denitrification was removing septic system and agriculturally derived N, but N from belowground leaking sewers was less susceptible to denitrification. N transformations were also observed in a storm drain (no natural drainage network) potentially due to organic carbon inputs. Overall, nonpoint sources such as atmospheric deposition, wastewater, and fertilizer showed different susceptibility to watershed N export. There were large changes in nitrate sources as a function of runoff, and anticipating source changes in response to climate and storms will be critical for managing nonpoint N pollution.