In addition to traditional sources, drained peat soils have been found to be a significant source of nitrogen in Estonia. As a result, supplementary measures are required to improve water quality in rivers. Modelling is a widespread method to select means for improving water quality. At present, modelling of nitrogen in rivers has been concentrated on the influence of agricultural activity. However, drained peat can increase nitrogen concentrations even without fertilization and farming activities. This investigation describes the attempt to model water quality in the watershed with a large share of drained peat soils. The results showed a good alignment between measured and modelled nitrate concentrations using the MACRO and the SOILN for MACRO models. Some measures to improve water quality were tested using these models.