Near-surface wind speeds have changed over recent decades, raising questions about the extent to which these changes are altering the vertical thermal structure of lakes and affecting lake food webs. Neo- and paleolimnological techniques were used to assess wind-driven changes in lake thermal habitat and resulting effects on primary producers in two lakes in Isle Royale National Park, an island archipelago located in Lake Superior, where wind speed has increased in recent decades. Responses in Siskiwit Lake, a large (16 km2 surface area), deep (Zmax = 49 m), oligotrophic lake, were compared to those of Lake Desor, a moderately large (4.3 km2) but shallower (Zmax = 13 m), mesotrophic lake. High-frequency sensor data suggested that changes in wind speed affected epilimnion thickness in both lakes synchronously (ρ = 0.7, p < 0.001). Diatom-inferred mixing depths suggested a coherent shift in both lakes to deeper mixing (an increase of 3 and 6 m) since 1920 (ρ = 0.8), which was correlated with an increase in regional wind speed during the 20th century at the decadal-scale in Lake Desor and Siskiwit Lake (ρ = 0.6 and 0.4, respectively). In Lake Desor, algal biomass declined as mixing deepened from 1920 to 1980, and then cyanobacteria and cryptophyte pigments increased from 1980 to present, a period of inferred stable and deep mixing. Algal pigment concentrations in Siskiwit Lake were unchanged as mixing depth deepened. Although changes in wind speed altered lake physical structure similarly, the ecological consequences of these changes differed between lakes and were most likely influenced by lake-specific variability in nutrient and light availability.