The geochemical record in lake sediments was investigated in four gravity-core collected sediment cores from Farmington Lake, a drinking-water reservoir, to understand the geochemical history in the reservoir, determine any potential effects on water quality, and evaluate watershed processes. Trace-element sediment chemistry of arsenic, copper, lead, manganese, and sulfur revealed variable patterns among the four cores suggesting fluctuating water inputs to the reservoir depending on known conditions in the watershed or effects of local geology, lake turnover, redox conditions, or evaporative conditions in the sediments. Manganese and sulfur concentrations in reservoir sediments compared with local groundwater and surface water chemistry indicate that reduction–oxidation mechanisms play an important role in the chemical variability identified in the sediments and that there may be direct interaction with groundwater in Farmington Lake. Results of mobility experiments showed that the majority of manganese and copper were released from sediments after reaction with acetic acid and that sulfur was primarily released after reaction with a bicarbonate solution. Scanning electron microscopy evaluation of sediments showed that the reservoir sediments are predominantly kaolinite and montmorillonite with barite, framboidal pyrite, and iron and manganese oxides within the clay matrices. In contrast to the sediment chemistry from nearby Aztec Drinking Water Reservoir #1, evidence of upstream mining and milling was not observed in the sediment chemistry of Farmington Lake. This is further confirmed through identification of diatom taxa from the sediment, where no taxa were indicative of sustained low pH or highly mineralized water entering the reservoir. The results of this study provide information about the geochemical mechanisms in a large drinking-water reservoir that can be used for management decisions and an understanding of the geochemical transport that occurs in a dynamic watershed.