The quantitative and qualitative depletion of water resources (both surface and groundwater) is closely related to the need to protect soils against degradation, rationalization of land use, and regulation of surface water runoff within the watershed area. Belgorod Oblast (27,100 km2), one of the administrative regions of European Russia, was chosen as the study area. It is characterized by a high activity of soil erosion (the share of eroded soils is about 48% of the total area of arable land). The development phase of the River Basin Environmental Management Projects (217 river basins from the fourth to seventh order) allowed for the proceeding of the development of an integrated monitoring system for river systems and river basin systems. The methods used to establish a geoecological network for regional monitoring include the selection and application of GIS techniques to quantify the main indicators of ecological state and predisposition of river basins to soil erosion (the share of cropland and forestland, the share of the south-oriented slopes, soil erodibility, Slope Length and Steepness (LS) factor, erosion index of precipitation, and the river network density) and the method of a hierarchical classification of cluster analysis for the grouping of river basins. An approach considering the typology of river basins is also used to expand the regional network of hydrological gauging stations to rationalize the national hydrological monitoring network. By establishing 16 additional gauging stations on rivers from the fourth to seventh order, this approach allows for an increase in the area of hydro-agroecological monitoring by 1.26 times (i.e., up to 77.5% of the total area of Belgorod Oblast). Some integrated indicators of agroecological (on the watershed surface) and hydroecological (in river water flow) monitoring are proposed to improve basin environmental management projects. Six-year monitoring showed the effectiveness of water quality control measures on an example of a decrease in the concentrations of five major pollutants in river waters.