Contamination of the trace elements (TEs) in the freshwater ecosystems is becoming a worldwide problem. This study was carried out to investigate the TEs contamination, and their associated health risk in Begnas Lake and Rupa Lake, Gandaki Province, Nepal. A total of 30 water samples were collected from both lakes during the pre-monsoon season in 2016. The samples were analyzed for the TEs including copper (Cu), lead (Pb), zinc (Zn), nickel (Ni), cobalt (Co), chromium (Cr), cadmium (Cd), manganese (Mn), cesium (Cs), and arsenic (As) using inductively coupled plasma mass spectrometry. The results exhibited that the mean concentrations of all the TEs were higher in Rupa Lake as compared to Begnas Lake except Pb. Principal component analysis and cluster analysis revealed that both the geogenic and anthropic sources were the major contributors of TEs in the lake water. Anthropic activities were considered to contribute the TEs like Zn and Mn in lake water mainly via agricultural runoff, while evaluating the risk of TEs on human health all the elements showed HQ < 1 and CR < 10−4 indicating currently very low health risk concerns. In good agreement with above, the water quality index (WQI) of the Begnas Lake and Rupa Lake was 2.67 and 5.66, respectively, specifying the lake water was safe for drinking and public health concern. This appraisal would help the policymakers and concerned stakeholders for the sustainable management of Ramsar listed freshwater lakes in the Himalayas.