As a result of reductions in sulfate deposition and changing climate, dissolved organic carbon (DOC) concentrations have increased in many lakes situated in forests of northeastern North America and northern Europe since the 1990s. Although this increase is well documented, the associated ecological implications remain unclear. In particular, DOC strongly influences the vertical temperature structure of lakes, with increasing DOC often leading to a shallower epilimnion. We investigated the effect of increased DOC concentrations on lake thermal structure using fossil diatom records from six remote Maine lakes. Sedimentary diatom profiles from three pairs of small (<0.5 km 2 ) lakes were compared, with each pair containing one lake with a documented significant increase in DOC and the other experiencing no change in DOC since the early 1990s. Lake thermal structure was inferred from changes in the relative abundance of Discostella stelligera and Aulacoseira species, two diatom taxa that are associated with changes in thermal stratification. The three lakes without increasing DOC showed no change in diatom-inferred mixing depth over the past few decades. Of the lakes with documented increases in DOC, two showed the highest turnover in diatom community structure over time. Profiles from both of these lakes also indicated directional change in diatom-inferred mixing depth over the past 20 years, but the direction of change differed. This study demonstrates that recent increases in DOC have the potential to alter the physical and biological structure of lakes, but that these responses may differ across lakes.