The ionic composition and salinity of Lake Manitoba and its late-glacial precursor, Lake Agassiz, changed significantly over the past 11 000 years. The paleochemical record reported here is based on modern analog environments of ostracodes identified in a new 14.5 m core from southern Lake Manitoba. The ionic composition of Lake Manitoba today is dominated by Na+, Cl−, and HC03−, with much less Ca2+, Mg2+, and K+. Evaporative concentration of modern Lake Manitoba water would lead to greater salinity and the near depletion of Ca2+ due to continued precipitation of calcite. During periods of highest salinity in the Holocene, however, Lake Manitoba supported Limnocythere staplini. Today this species inhabits waters in which [Ca2+] > [HCO3−], including springs associated with groundwater in Paleozoic bedrock discharging into Lake Winnipegosis (and eventually, after much dilution, into Lake Manitoba). Further complicating the Holocene record are intervals containing Limnocythere friabilis that suggest periodic influxes of dilute water, probably from the Assiniboine River, which bypasses Lake Manitoba today. The variations in Holocene paleochemistry indicated by the ostracode record imply changes in the proportion of overland flow plus precipitation relative to groundwater inputs to Lake Manitoba, independent of changes in evaporation relative to precipitation.