Coimbatore is one of the industrial cities in Tamil Nadu, India, which has been experiencing rapid urbanization and population growth. Coimbatore is also known for its unique freshwater lakes environment and serves as a rich ecosystem. However, the assessment of heavy metal levels in aquatic environments is limited. This study was aimed to investigate physicochemical parameters, heavy metals level and sources, and ecotoxicity in sediments collected from five different lakes in Coimbatore. The concentrations of heavy metals (Cr, Cu, Zn, As, Cd, and Pb) in sediments were determined by Inductive Coupled Plasma-Mass Spectroscopy (ICP-MS). Hg level was measured using Advanced Mercury Analyzer (AMA). The determined heavy metal concentrations in sediments varied significantly according to the lake location and consistent with local human linked anthropogenic activities. The metal concentrations in urban lakes were exceeding both the Sediment Quality Guidelines (SQGs) and the probable effect levels” (PELs) mostly; e.g., in sediments from the Lake Ukkadam, the values of 5.08 and 203.32 mg kg-1 dry weight were observed for Hg and Cu, respectively. The ecotoxicity test with ostracods exposed to the sediment samples revealed that mortality rate ranged between 6 and 23% for countryside lakes and 28 and 88% for the lakes within urban Zone. We used Spearman rank-order correlation and Principal components analysis (PCA) to assess the sources of pollutants and if they related to anthropogenic pressure and eutrophication of lakes. The main sources of heavy metals from studied lakes differed significantly. Urban and industrial effluents were dominant sources in urban lakes. Agricultural runoff, domestic wastes, and natural weathering were responsible for the metal sources in country lakes. This study provides baseline information on the heavy metal pollution status of sediments in the freshwater lakes in Coimbatore, which will be useful for pollution control measures to prevent possible metal sources on these lakes and impose appropriate management practices and continuous monitoring by relevant authorities.