This doctoral thesis aims to develop an innovative integrated water quality management model of a rural transboundary river basin within integrated water management to achieve the environmental goals of the river basin. The developed model was tested on Slovenia and Croatia's rural transboundary Sutla River basin. The model is based on the implementation of the DPSIR approach with ArcGIS to create a comprehensive analysis, to define the key problems of the river basin, as well as the key sources of pressure in the river basin. The SWAT mathematical model was implemented to be suitable for smaller rural transboundary river basins and was selected for the quantification of pressures. Different scenarios were modelled with the application of basic and additional measures, namely: current state scenarios, past state scenarios "with" and "without" the Vonarje reservoir /Sutlansko lake, and future state scenarios "with" and "without" the Vonarje reservoir/Sutlansko lake including the impacts of climate change. An analysis was made for the scenario of the current state, critical sub-basins with "hot spots" of nutrient and sediment pressures were singled out, and supplementary "tailor-made" measures for the river basin were applied. The results of the developed innovative model application and the effectiveness of the proposed measures indicate the possibility of applying the mentioned approach and applied measures for all sub-basins and all scenarios. The developed innovative model enables the improvement of water quality management, and with the developed/improved methods and methodologies in it, it can be applied to other river basins of water bodies of the Pannonian ecoregion, as well as to other regions with a continental climate. Based on new knowledge about the processes in the river basin with the developed innovative model, it is possible to create an assessment of the risk of not achieving the environmental goals of the river basin, as well as the risks of achieving good water status and water eutrophication.