Anthropogenic contamination is damaging the fragile Western Ghats making it necessary to understand the historical pollution. Radiocarbon dated sediment core covering the past 753 years is investigated to reconstruct the paleoclimate and paleotoxicity in Honnamanakere Lake, southern India. Increased sedimentation, weathering, organic carbon, and clay fraction during the medieval and modern warm periods indicate stronger southwest monsoon rainfall than during the little ice age. A decrease in silt content at the core location during warm periods suggests high lake levels. Cr, Cu, Zn, Pb, Hg except Ni content is increasing from bottom to top of the core. Multivariate statistics suggest natural sources for organic carbon and weathering products, agrochemical sources for Cr, Cu, Zn, atmospheric sources for Pb and Hg, and mixed sources for Ni. The enrichment factor and geoaccumulation index are increasing from the bottom to top of the core. Cr and Ni are significantly enriched and extremely contaminated and exhibit the most severe threat to the water body. The toxic risk index of Cu, Zn, Pb, and Hg suggests no toxic risk, Cr suggests low toxic risk and Ni suggests moderate toxic risk. The combined toxic risk of heavy metals suggests considerable to very high toxic risk. The mean probable-effects-levels quotient suggests heavy metals are posing a 49% toxic risk to the water body and its biota. In the sediment core, there is an increase in heavy metals enrichment, accumulation, and toxic risks during the past 300 years which is synchronous with the anthropogenic Industrial era.