Diatom assemblages in recent versus pre-industrial sediments were examined in 40 relatively undisturbed lakes from the Experimental Lakes Area (ELA). The ELA region of northwestern Ontario receives low amounts of acidic deposition and the lakes have been minimally disturbed by watershed development or other human activities. Consequently, this region represents an important location to detect possible changes in lakes due to climate change. In over half of the lakes, planktonic taxa (especially Discostella stelligera) increased between 10 and 40% since pre-industrial times. Changes in diatom assemblages are consistent with taxa that would benefit from enhanced stratification and a longer ice-free season. We hypothesized that there should be a relationship between stratification and measured chemical and physical characteristics of the study lakes. Multiple correlation analysis was undertaken to see the relationship between planktonic taxa and D. stelligera since pre-industrial times and the physical and chemical characteristics of the study lakes. Lake depth was consistently identified as an important variable. The timing of the increase in planktonic taxa within cores from these lakes will be needed to rule out other possible regional changes that may also be occurring in the ELA region. © 2011 Springer Science+Business Media B.V.