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This study assessed the level of potentially toxic trace metals (PTMs), seasonal variations, and their possible sources from the surface water and lake-bed sediment of Panchpokhari lake series, an alpine and glacial lake at 4160 m a.s.l. in Central Nepal. The lake series have five lakes, with Lake-1 larger than others. So, Lake-1 was investigated thoroughly during pre-monsoon and post-monsoon seasons. Sediment core was collected from the deepest basin of the Lake-1 during pre-monsoon. Most of the PTM concentrations were higher in the pre-monsoon season; however, Sc, Cr, Cu, Zn, As, and Ag were higher in the post-monsoon. This is an indication that the lake has been impacted either by natural or long-range transported atmospheric pollutants. Ti, Sb, and Ag had extremely high enrichment factor (EF) in waters, whereas Cd, Zn, and As had high EF in sediments indicating that these metals originated from anthropogenic sources. Furthermore, PTM concentrations in the sediment were in the increasing order of Hg