Fresh water scarcity is considered a significant component, and potentially one of the most critical, of global climate change. With the rapid development of industry, there is an increasing risk of freshwater contamination by heavy metals (HMs). The danger of HM pollution is also attributed to their accumulation, which can subsequently become a source of secondary pollution in aquatic environments. In the Lake Gusinoe basin, located in Russia, concentrations of HMs were measured in both water and bottom sediments within the lake area, as well as in inflowing and outflowing watercourses. Ecological risk indices were also calculated for the Gusinoe basin. Our results showed that the average concentrations of Fe, Zn, Cr, Ni, Cd, and Pb in the water did not exceed the maximum allowable concentrations (MACs) set by Russian national standards and WHO standards, while the concentrations of Mn and Cu exceeded the corresponding MACs during winter, spring, and autumn possibly due to decomposition of aquatic vegetation and influx from groundwater sources. The average concentrations of the investigated HMs in the BSs did not exceed the background values. The water hazard index indicated a low risk for all samples in the lake water area. For all BS samples, the geoaccumulation index (Igeo) and the Pollution Load Index (PLI) indicated low pollution levels, while the values of the Enrichment Factor (EF) and the Contamination Factor (CF) indicated moderate pollution in the central part of the lake. The Ecological Risk Factor (Er) for Cu in BSs at points near major settlements and in the Tel River indicated moderate pollution. The Potential Ecological Risk Index (RI) in all investigated BS samples indicated a low risk of contamination.