This paper presents the results of testing the applicability of the MIKE Basin model for simulating the efficiency of scenarios for reducing water pollution. The model has been tested on the Olšava River Basin (520 km2 ) which is a typical rural region with a heterogeneous mix of pollution sources with variable topography and land use. The study proved that the model can be calibrated successfully using even the limited amount of data typically available in rural basins. The scenarios of pollution reduction were based on implementation and intensification of municipal wastewater treatment and conversion of arable land on fields under the risk of soil erosion to permanent grassland. The application of simulation results of these scenarios with proposed measures proved decreasing concentrations in downstream monitoring stations. Due to the practical applicability of proposed measures, these could lead to fulfilment of the water pollution limits required by the Czech and EU legislation. However, there are factors of uncertainty that are discussed that may delay or limit the effect of adopted measures in small rural basins.