Lake Naivasha, Kenya's second-largest freshwater body is a wetland of international ecological importance and currently subjected to unprecedented anthropogenic influence. The study aims to chronologically reconstruct the main human activities and background weathering reactions that govern metal mobilizations into the lake and their potentially adverse effects on its ecological status. We combine extensive geochemical analyses (major, trace elements, Zn-Pb isotope ratios) in a dated lake sediment record and catchment rocks with remote sensing techniques. Downcore geochemical variations reflect natural ecosystem destabilizations occurring as early as the first half of the 20th century. These coincide with changes towards less radiogenic Pb-isotope values which persist towards the top of the core (206Pb/207Pb = 1.243 at core base ∼1843, to 206Pb/207Pb = 1.225 at ∼1978). We interpret the land-clearance for agricultural purposes on the Aberdare Range and documented early aviation activities as possible vectors of this early Pb-isotope excursion. The overlapping Pb-isotope signatures between sediment sources and anthropogenic contributions challenges a straightforward deconvolution of the two. Our conservative model calculations suggest, nevertheless, that an addition of up to ∼1.8 % Pb-gasoline influx to the total Pb flux, peaking in the 1980s is able to explain the Pb distribution trend. Homogeneous Zn-isotope compositions in sediments deposited until ∼1970s (δ66/64Zn = 0.216–0.225 ‰) do not follow major hydro-climatic events or anthropogenic forcing but likely reflect lake-specific natural cycling. Subsequent higher variations to both heavier (up to δ66/64Zn = 0.242 ± 0.005 ‰) and lighter (down to δ66/64Zn = 0.184 ± 0.003 ‰) Zn-isotope values are contemporaneous with intensification of large-scale horticultural industry in the catchment. Together with supporting indicators, the lighter Zn-isotope compositions in youngest analysed sediments (21st century) are attributable to increased biological productivity (algal blooms) and ongoing lake eutrophication. Our study demonstrates the applicability of the heavy metal isotope tool to reconstruct human influences on lake environments with complex geological settings such as the East African Rift System.