The basin of the small river studied here (the Vezelka River, Belgorod Oblast of European Russia) is located within an urban area (22% of the basin). This circumstance determines its specificity as an object of synergetic anthropogenic impact. The purpose of the work was to develop and test approaches to the integral assessment of the hydroecological situation both in the watershed and riparian zones based on hydrological, hydrochemical, and hydrobiological data and estimates of soil erosion, river water quality, and the pollution of river bottom sediments. The selection of the Vezelka River and its watershed for the study was due to the presence there of two water intakes for a town with a population of 2439 people per sq. km, repeated bottom deepening in the riverbed, and the fact that there is a single regional small-river hydrological station (although there are 567 rivers < 25 km long in Belgorod Oblast). Analysis for 1951–2021 showed a steady decline in water discharge since 1991; thus, over the past three decades, the discharge has decreased by 2.4 times. The reduction in the length of the river network of the study region by 38% over the past 250 years and the assignment of water (at 10 gauging stations) to 3–4 quality classes (extremely and heavily polluted) indicated the exhaustion of the possibilities for the self-purification of the river water. These estimates for large and medium rivers were clearly confirmed by the investigation of the water in the small river studied. In the summer low-water periods, the maximum allowable concentrations in fishery water bodies were exceeded by 2–10 times in terms of Cu, Fe, ammonium, oil, and biochemical oxygen demand. The reconstruction of the floodplain–channel subsystem of river–valley landscapes was substantiated as the final stage of the concept of basin nature management, replacing the continuous deepening of the channel without proper erosion control measures in the watershed area and the organization of buffer zones along the river banks.