Human impacts on freshwater ecosystems are pervasive, but the short and discontinuous nature of most datasets limits our ability to understand the controls on water quality and effectively manage freshwater resources. We examine change in Lake Mendota (Madison, Wisconsin) over the last two centuries by pairing analyses of a sedimentary archive with the site's > 100 yr limnological record. We show that eutrophication of the lake, evident as an abrupt shift in sediment composition, began in the late 19 th century following the intensification of urban and agricultural land use in the watershed. Efforts to address deterioration of lake water quality, including the removal of point-source pollutants and biomanipulation, have had a measurable influence on sediment composition and water clarity. Since the early 1980s, quasi-seasonal cycles of phytoplankton blooms have induced calcite precipitation, leaving distinct laminations in the sedimentary record. These "whiting events" evidently did not accumulate in lake sediments until the late 20 th century, indicating that efforts to remediate water quality have shifted the lake to a new ecosystem state. Calcite whitings can improve water quality in eutrophic lakes by coprecipitation with phosphate, increasing phosphorus (P) burial in lake sediments. Using long-term limnological records, we report negative correlations between calcite saturation indices and P in lake surface waters and show that calcite whitings could partially explain recent P decline in Lake Mendota surface waters. Our study reveals a previously uncharacterized potential control on water quality in this eutrophic lake and demonstrates the benefit of coupling long-term limnological data with sedimentary records.