The present study investigates the anthropogenic metal input into the lake system, the toxic metal pollution in the sediments of Kodaikanal Lake. Surface sediment samples were collected at seven locations to represent its spatial variability within the lake. Samples were subjected to analyze for Fe, Co, Cr, Mn, Ni, Zn, Cd, Cu, Ag, Pb, Hg, and As by energy dispersive X-ray fluorescence (EDXRF) and their concentrations in lake sediments range from 102,000–109,000, 561–2699, 292–544, 211–482, 79–163, 57–265, 57–74, 37–92, 46–59, 20–97, 19–30, to 13–24 mg/kg, respectively. The sources of pollution were inferred through spatial and statistical analyses. Most of the toxic metal contents in the sediments are found to exceed the background concentration in all locations. The enrichment factor (EF) and index of geoaccumulation (Igeo) of Hg, Co, Cd, and Ag showed that sediments of Kodaikanal Lake exhibit the probability of anthropogenic influence. The significant Pearson’s correlation coefficient is also suggesting that they probably originated from the same source of occurrence. The contamination factor and degree of contamination of the Kodaikanal Lake sediments are strongly polluted in terms of most of the examined metals. The study also provides environmentally significant information about anthropogenic influence on the lake sediments.