We applied a diatom-based thermal stratification index to sediment cores from three lakes in the northeast USA to evaluate the influence of lake morphometry and within-lake processes on diatom responses to climate change. The three lakes all had surface area [5 km 2 and experienced the same regional declines in wind speed and progressively earlier ice-out dates, but differed in morphometry, particularly surface area and mean depth. We coupled this paleolimnological approach with contemporary ecological measurements to validate the use of two indicator species (Aulacoseira subarctica (O. Müller) Haworth and Discostella stelligera (Cleve & Grunow) Houk & Klee) in the stratification index. D. stelligera was abundant during stratified conditions in Tunk Lake and Sebago Lake, but not in Lobster Lake. Diatom-inferred stratification shifted to shallower and/ or longer duration in Tunk Lake starting in the late nineteenth century, and continued to become shallower over much of the twentieth century. A shift to shallower and/or longer duration was also apparent in Sebago Lake starting around 1850, after which the index suggested little change, even though ice-out occurred 30 days earlier in 2000 than in 1807 and wind speed began to decline in the 1960s. This lake has very slow sedimentation rates, experiences regular seiches, and has D. stelligera present during circulation and stratified periods. These factors may smooth stratification-driven diatom responses. Contemporary ecological measurements did not support the application of the stratification index in Lobster Lake because D. stelligera bloomed only during spring turnover. In Lobster Lake, the relative abundances of D. stelligera in the sediment record showed some variation over time, were generally lower in periods with earlier iceout in the region, and have been lower since the 1980s. Our results highlight the different responses recorded in the sediments of three large lakes in the same region to climate-driven changes and support the use of indicator species in reconstructing lake thermal stratification patterns when paired with site-specific morphometric and ecological data.