A greater appreciation of biotic responses to environmental changes is warranted in small, shallow lakes because of the high number of these habitats, and their unique contributions to regional biodiversity. Furthermore, recent water chemistry monitoring data show that shallow lakes in Ontario are sensitive and have responded significantly to environmental stressors such as acid deposition and lake water calcium decline. Here, we use paleoecological techniques to examine cladoceran assemblages in modern and pre-industrial sediments of 30 shallow lakes to determine the key environmental gradients that influence present-day assemblages, and to assess how assemblage structure has changed since pre-industrial times (pre-1850s). Redundancy analysis of present-day cladoceran assemblages and key environmental variables identified lake surface area and Secchi depth as significant predictors of assemblage composition. In our data set, Secchi depth was not correlated to water clarity but rather to macrophyte cover, suggesting that cladoceran assemblages were highly influenced by habitat structure. In contrast to nearby, deeper lakes, where pelagic cladoceran taxa have changed significantly in relative abundance over time, cladoceran assemblages in present-day and pre-industrial sediments of shallow lakes did not differ significantly in composition. While the specific reasons for this muted response are unknown, we hypothesize that: (1) littoral taxa may be less sensitive to low Ca concentrations, or ecological thresholds have not yet been crossed or are lower for littoral taxa; (2) calcium availability may vary spatially within shallow lakes, and this is not captured in a single measure of water chemistry from the centre of the lake; and/or (3) habitat structure is more important than water chemistry as a predictor of assemblage composition in these study lakes, and this has not changed significantly over time.