A detailed mass balance on nitrogen was carried out in shallow and hypertrophic Lake Søbygård during 4.5 years before through 2.5 years after a 36 % reduction in nitrogen loading. Annual mean loss rate of nitrogen was 159–229 mg N m−2 d−1 before the loading reduction and 125 mg N m−2 d−1 after. In spite of a short hydraulic retention time (18–27 days) the proportion of nitrogen loading lost in the lake was high (38–53 %) and not affected by changes in loading. Calculated denitrification accounted for 86–93% of the loss rate, while 7–14% was permanently buried. Marked seasonal variations in the loss percentage were found during the season, ranging from 23 % in first quarter to 65 % in third quarter. The seasonal variation in the loss percentage of nitrogen showed a hysteresis like relationship to temperature, with a high percentage in fourth quarter. This suggests that the amount of available substrate, which mainly consists of sedimentated phytoplankton, accumulated during summer, is an important regulating factor. The ability of various published input-output models to predict the observed changes in in-lake nitrogen concentration in Lake Søbygård was tested. This study has further confirmed that small lakes with short retention and high nitrogen loading may significantly reduce the nitrogen loading of downstream aquatic environments.