The intensive use of soil and water resources results in a disbalance between the environmental and economic objectives of the river basin. The water quality management model supports good water status, especially downstream of dams and reservoirs, as in the case of the Sutla/Sotla river basin. This research aims to develop a new, improved integrated water quality management model of rural transboundary basins to achieve environmental objectives and protection of the Natura 2000 sites. The model uses river basin pressure analysis to assess the effects of climate and hydrological extreme impacts, and a programme of basic and supplementary measures. The impact assessment of BASE MODEL, PAST, and FUTURE scenarios was modelled using the soil and water assessment tool (SWAT) based on land use, climate and hydrological data, climate change, presence or lack of a reservoir, and municipal wastewater and agriculture measures. Eight future climate change scenarios were obtained with optimistic (RCP4.5) and pessimistic (RCP8.5) forecasts for two periods (2020–2050 and 2070–2100), both with and without a reservoir. The model shows that the most significant impacts on the waterbody come from the nutrients and sediment hotspots, also shows the risk of not achieving good water status, and water eutrophication risk. The modelled average annual increase in sediment is from 4 to 25% and in total N from 1 to 8%, while the change in total P is from −5 to 6%. The conducted analysis provides a base for the selection of tailor-made measures from the catalogue of the supplementary measures that will be outlined in future research.