In the last 5 years Russia developed Schemes of Integrated Use and Protection of Water Objects (SKIOVO) aiming at remediating and maintaining water resources quality. The main limitation of the schemes is seen in their large spatial scale, which is determined by the available environmental monitoring data. The meso-scale catchments are usually ungauged, which does not allow monitoring and management of water quality on the respective scale and thus they are not included in the schemes. This can have severe consequences, if the catchment is used for drinking water supply (DWS) from surface waters. This is shown in the example of the Nytva river basin, where raw water is extracted from the eutrophic Nytva reservoir for DWS. The solution of the problem is seen in the application of structured water quality mitigation measures, included in the basin management plan. A method to develop such a plan is presented here. The preliminary results of system screening (identification of problems and drivers) and material flow analysis (MFA) have shown that the reservoir is hypertrophic and the probable drivers are emissions from cattle breading, point sources and erosion from arable land. Apart from first measurements, soft factors and the problem of eutrophication identification are discussed, pointing out the need for further studies with regard to eutrophication in the reservoir and the analysis of stakeholders and material flow.