The monsoon season in South Korea has great influences on biogeochemical and hydrological processes in the entire country, but is specifically of concern in the Soyang lake watershed, the main drinking water reservoir for the 20-million-people metropolis Seoul. Therefore, water quality and nitrate concentration control in Lake Soyang is of high public priority. The Haean catchment is the most prominent agriculture-dominated sub-catchment of the Soyang lake watershed. It is a complex terrain influenced by extreme rain events and non-point nitrate sources. In this investigation we used input-output calculations and a stable isotope approach to quantify and determinate the origin of nitrate inputs into the rivers that later flow into the lake. During pre-monsoon and monsoon seasons in 2013 and 2014 we measured daily rainfall and river water discharge within the Haean catchment and collected rain, river water and groundwater samples in order to analyze nitrate concentrations and nitrate nitrogen and oxygen isotope abundances. Furthermore, we collected nitrogen fertilizers as applied in the catchment. Heavy monsoon events, as in 2013, were the most pronounced drivers of nitrate leaching being responsible for >80% of the nitrate output in the river runoff. On the other hand, an almost missing summer monsoon in 2014 drove the nitrate runoff in a different manner, being responsible for only 0.4% of the total nitrate nitrogen river discharge in the previous year. Results of nitrate nitrogen and oxygen isotope abundance analyses suggest soil microbial nitrification as the most important contributor to the nitrate in the river runoff. In addition, nitrate from groundwater partially affected by microbial denitrification contributed to the nitrate in the runoff due to river-aquifer exchange fluxes during the monsoon season. Direct leaching of nitrate from mineral fertilizers and atmospheric nitrate deposition were obviously only minor contributors to the nitrate in the runoff.