Lake St. Croix is a natural impoundment located at the southern end of the St. Croix River and is part of the St. Croix National Scenic Riverway. Land use changes beginning at the time of European settlement have resulted in nutrient runoff, eutrophication, and periodic oxygen depletion in the hypolimnion. Establishing sound lake management practices requires knowledge of historical or baseline conditions, which can be provided by paleolimnological studies. Remains of Chironomidae and other Diptera in lake sediments have been shown to be reliable indicators of past hypolimnetic oxygen conditions. Cores from two sub-basins in the lake were collected in 2005. Chironomid analysis indicates that shifts in species assemblages occurred corresponding to the time of European settlement, and later development and eutrophication of the lake. Species such as Chironomus, which is tolerant of low oxygen levels, increased in relative abundance. Volume-weighted hypolimnetic oxygen concentrations (VWHO) were estimated using a transfer function developed for southern Ontario. The average VWHO decreased by 1 to 2 mg/L after European settlement. Lowest oxygen concentrations occurred in the post-WWII era. This study, in conjunction with other historical and paleolimnological work on Lake St. Croix will provide baseline data for setting management goals and evaluating results.