Climate disrupts aquatic ecosystems directly through changes in temperature, wind, and precipitation, and indirectly through watershed effects. Climate-induced changes in northern lakes include longer ice-free season, stronger stratification, browning, shifts in algae, and more cyanobacterial blooms. We compared retrospective temperature-depth relationships modeled using MINLAKE2012 with biogeochemical changes recorded in sediment cores. Four lakes in Voyageurs National Park (VOYA) and four lakes in Isle Royale National Park (ISRO) were studied. Meteorological data from International Falls and Duluth, Minnesota, were used for VOYA and ISRO, respectively. Model output was processed to analyze epilimnetic and hypolimnetic water temperatures and thermal gradients between two periods . Common trends were increased summer epilimnion temperatures and, for deep lakes, increased frequency and duration of thermoclines. Changes in diatom communities differed between shallow and deep lakes and the parks. Based on changes in benthic and tychoplanktonic communities, shallow lake diatoms respond to temperature, mixing events, pH, and habitat. Changes in deep lakes are evident in the deep chlorophyll layer community of Cyclotella and Discostella species, mirroring modeled changes in thermocline depth and stability, and in Asterionella and Fragilaria species, reflecting the indirect effects of in-lake and watershed nutrient cycling and spring mixing.