Lakes are critical resources that support the ecological balance and provide essential services for human and environmental well-being. However, their quality is being increasingly threatened by both natural and anthropogenic processes. This study aimed to assess the water quality and the presence of heavy metals in 15 lakes in the Vidarbha and Marathwada regions of Maharashtra, India. To understand the extent of pollution and its sources, the physico-chemical parameters were analyzed which included pH, turbidity, total hardness, orthophosphate, residual free chlorine, chloride, fluoride, and nitrate, as well as heavy metals such as iron, lead, zinc, copper, arsenic, chromium, manganese, cadmium, and nickel. The results revealed significant pollution in several lakes, with the Lonar Lake showing a pH value of 12, exceeding the Bureau of Indian Standards’ (BIS) limit. The Lonar Lake also showed elevated levels of fluoride having a value of 2 mg/L, nitrate showing a value of 45 mg/L, and orthophosphate showing a concentration up to 2 mg/L. The Rishi Lake had higher concentrations of nickel having a value of 0.2 mg/L and manganese having a value of 0.7 mg/L, crossing permissible BIS limits. The Rishi Lake and the Salim Ali Lake exhibited higher copper levels than other lakes. Cadmium was detected in most of the lakes ranging from values of 0.1 mg/L to 0.4 mg/L, exceeding BIS limits. The highest turbidity levels were observed in Rishi Lake and Salim Ali Lake at 25 NTU. The total hardness value observed in the Kharpudi Lake was 400 mg/L, which is highest among all the lakes under study. The spatial analysis, which utilized remote sensing and GIS techniques, including Sentinel-2 multispectral imagery for land use and land cover mapping and Digital Elevation Model (DEM) for watershed delineation, provided insights into the topography and drainage patterns affecting these lakes. The findings emphasize the urgent need for targeted management strategies to mitigate pollution and protect these vital freshwater ecosystems, with broader implications for public health and ecological sustainability in regions reliant on these water resources.