Water pollution related to trace elements has emerged as a worldwide concern owing to their increasing concentration and damages to the aquatic ecosystems. The water ecosystem of Manchar Lake situated in the arid region of Pakistan has also been degraded and posing a severe health risk to the dependent communities. This study aims to investigate the seasonal variability in the influx of trace elements (As, Cd, Cr(III), Cr(VI), Cu, Fe, Hg, Mn, Ni, Pb, and Zn) into the lake during premonsoon, monsoon, and post-monsoon seasons and its consequential health risks. The highest mean concentrations (μg/l) of As (43.2), Cr(III) (101.4), Zn (41), Cu (43.12), Fe (318), Cd (18.5), Mn (27.2), Ni (99.7), Pb (65.91) and Hg (6.8) have been observed in pre-monsoon and Cr(VI) (0.2) in monsoon seasons. The elements exceeding safe limits in pre-monsoon season are As, Cd, Cr(III), Hg, Ni, and Pb, while in monsoon season As, Cd, Ni, and Pb exceed the limit. Evaluation of the degree of contamination depicted high levels of pollution in pre-monsoon and monsoon seasons and the Heavy Metal Evaluation Index indicated a high level of pollution in pre-monsoon, medium in monsoon, and low in the postmonsoon season. The study revealed that oral consumption of lake water potentially causes carcinogenic and non-carcinogenic health risks. However, potential dermal related health risks associated with these metals concentrations in water are within the tolerable ranges. The findings of this study suggest prompt actions to control these pollutants influx into the lake.