Toxic trace metals in lacustrine sediments are of major concern since they can be hazardous to biota and human health. A high-resolution multiproxy study, including trace metals and major elements (measured by ICP-MS and XRF), total organic carbon, mineral carbon, Hydrogen Index, Oxygen Index, and C/N ratios, was performed on a sediment core from Vidy Bay in Lake Geneva. This bay has been affected by hazardous compounds released via the sewage effluent of a major wastewater treatment plant (WWTP). Anthropogenic trace metals, such as Pb, Cd, Cu, Zn, and Hg, increased following the industrial revolution in Europe. The highest amounts of these toxic metals, together with Ni, Cr, Co, Ag, Bi, and Fe, were recorded in sediments from 1964, the date of the WWTP implementation. During this period, all trace elements exceeded the sediment quality guideline “probable effect concentration” (PEC), with the following maximum concentrations (in mg /kg): Pb 4000, Cd 23, Cu 1200, Zn 8600, Hg 11, Ni 140, Cr 270, Ag 130, and Bi 310. The geochemistry of detrital elements (Al, Si, Ca, Ti, K, Zr, Rb, and Sr), as well as S, Fe, P, and the nature and quality of organic matter were clearly also affected by the effluent. The sedimentary record revealed that, after some improvements in the wastewater treatment processes and the relocation of the outlet pipe, the sediments tended to return to concentrations similar to those prevailing before the WWTP implementation. However, despite the reduction in the contamination load from the WWTP, which could be reinforced with the construction of a new plant in the near future, the sediments deposited in Vidy Bay represent a major contaminant legacy that constitutes a potential threat to the lake biota in the case of sediment remobilization.