To determine how climate-induced changes in hydrology and water level may affect the trophic state (productivity) of stratified lakes, two relatively pristine dimictic temperate lakes in Wisconsin, USA, were examined. Both are closed-basin lakes that experience changes in water level and degradation in water quality during periods of high water. One, a seepage lake with no inlets or outlets, has a small drainage basin and hydrology dominated by precipitation and groundwater exchange causing small changes in water and phosphorus (P) loading, which resulted in small changes in water level, P concentrations, and productivity. The other, a terminal lake with inlets but no outlets, has a large drainage basin and hydrology dominated by runoff causing large changes in water and P loading, which resulted in large changes in water level, P concentrations, and productivity. Eutrophication models accurately predicted the effects of changes in hydrology, P loading, and water level on their trophic state. If climate changes, larger changes in hydrology and water levels than previously observed could occur. If this causes increased water and P loading, stratified (dimictic and monomictic) lakes are expected to experience higher water levels and become more eutrophic, especially those with large developed drainage basins.