We used high-resolution diatom-based paleolimnological techniques to assess the effects of shoreline development and recent climate warming on three large embayments of Georgian Bay, Lake Huron (two impacted and one minimally impacted by shoreline development). The sedimentary diatom assemblages recorded subtle shifts at the impacted sites (North and South Bays) as a result of the establishment of permanent settlements and recreational resorts around the turn of the 20th century. No turn-of-the-century changes were observed at the reference site (Tadenac Bay). The abrupt increase in epiphytic Cocconeis placentula and benthic fragilarioid taxa during the 1950s at the shallower impact site (South Bay) was likely due to increased habitat provided by macrophytes. The increase in relative abundances of pennate (Asterionella formosa and Fragilaria crotonensis) and/or small centric (Cyclotella ocellata, C. comensis, and C. gordonensis) planktonic diatoms across the three sites after the 1970s suggests that recent warming-mediated changes to thermal properties (and related effects) are driving biological changes in these embayments. These recent diatom compositional changes are consistent with similar trends reported across Ontario and the Laurentian Great Lakes, where warming and its effects on aquatic ecosystem processes often favor small-celled centric diatoms. Differences in the timing and nature of diatom responses to similar environmental stressors across the three embayments highlight the importance of understanding site-specific characteristics when interpreting changes in diatom assemblages in paleolimnological records from the Laurentian Great Lakes.