N-nitrosodimethylamine (NDMA) and N-nitrosomorpholine (NMOR) and their specific precursors (N,N-dimethylformamide [DMF] for NDMA and morpholine [MOR] for NMOR) were widely identified in runoff of urban area around the southern Lake Biwa basin, Japan. It was thought that this runoff might constitute a non-point source of the four compounds in rivers and sewage treatment plants (STPs) during heavy rainfall events. We investigated the spatiotemporal patterns of NDMA, NMOR, DMF and MOR in runoff and rivers in rainy days. NDMA and NMOR were detected in concentrations of up to 295 ng/L, while DMF and MOR were detected in concentrations of up to 33.7 µg/L. Continuous sequential sampling over periods of 24 or 48 h at the largest STP in the study area revealed that the four compounds in the primary effluent (PE) each had higher mass fluxes during heavy rainfall events than on dry days. This phenomenon might be contributed to non-point sources (e.g., runoff) from infiltration/inflow related to rainwater into sanitary sewers. Moreover, the four compounds were confirmed to have higher mass fluxes in the final effluent of the STP during periods of PE bypass (1.3–1.7 times for NDMA, NMOR, and MOR; over 200 times for DMF; on average) than that on dry days because of increasing inflow during heavy rain than during periods without PE bypass in dry weather.