An integrated approach, combining groundwater flow and transport modelling with observed nutrient concentrations, was used to estimate mass discharge from a small crop field and surroundings via groundwater to an oligotrophic flow-through lake (Lake Hampen). Concentrations in groundwater discharging from the crop field were 70 times higher than in groundwater from forest areas. The crop field, only covering 4.5% of the discharging catchment, was responsible for a groundwater discharge of 16.2 ton nitrate/yr. Discharge via groundwater from the remaining part of the catchment was only 672 kg nitrate/yr for 2008. The study shows that both spatial heterogeneity for seepage and variation in solute concentration within the discharging aquifer, should carefully be investigated, if correct lake mass budgets are to be made.