The fabric of the Antarctic lacustrine system has a crucial role in assimilating the anthropogenic inputs and mitigating their long time impacts on climate change. Here, we present the changes in the concentrations of major ions and trace metals in the surface water of the lacustrine system to understand the extent of anthropogenic impacts from the adjacent Schirmacher Hills, East Antarctica. The results show that the land-locked lakes (closed-basin lakes surrounded by topographical barriers such as mountains or bedrock formations) in the region have a moderate enrichment in elemental concentrations compared to the pro-glacial lakes (marginal freshwater bodies that form at the terminus of a glacier or ice sheet). The water quality index (WQI: 7.58–12.63) and pollution evaluation index (PEI: 1.36–2.35) remained normal, indicating that the water in these lake are of good quality. However, a significant correlation between lithogenic elements (Al, Fe) and potentially toxic elements (Cd, Cr, and Ba), suggests an increase in the anthropogenic impacts. Based on the principal component analysis (PCA), the source of trace metals to the lacustrine systems appears to be the surrounding environment, followed by aerosol dust particles. Hierarchical cluster analysis (HCA) revealed that regional topography significantly impacts the supply of major ions/trace metals to these lakes. The present study provides baseline data and can be used to estimate and forecast future local and/or global anthropogenic contaminations in the lacustrine system of Schirmacher Hills, East Antarctica. Moreover, the presence of research stations (Maitri and Novolazarevskaya), tourist activities, and the potential for anthropogenic stressors necessitate continued monitoring and impact assessment programs within the Schirmacher Hills lacustrine systems. These programs are crucial for safeguarding this pristine ecosystem from future environmental disturbances under a changing Antarctic climate, as mandated by the Antarctic Treaty System and the Indian Antarctic Act.