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A paleolimnological approach was used at 45 mostly remote, low-nutrient lakes in New Brunswick (NB), Canada, to determine bioindicator responses and lake sensitivity to post twentieth century environmental change. From each undated core we assessed zooplankton (Cladocera) change between discrete time periods using related assemblage metrics, including the rise of Bosmina sp., cladoceran richness, and average assemblage body size. Cladocerans from a pre-industrial interval (20-20.5 cm) were compared to those from a present-day interval (0-0.5 cm). Lakes were then classified as either high- or low-sensitivity based on assemblage metrics, and sensitivity group differences in physical-chemical measures were tested for significance. Compared to pre-industrial times, Bosmina sp. relative abundance increased in 33 of 43 lakes (75% of lakes surveyed) by on average 20%. Body size and rarefied species richness of assemblages decreased significantly. These ecological shifts detected at an important intermediate trophic level are attributable to indirect effects of climate change, although we cannot rule out shifts in fish predation and littoral habitat as additional structuring factors. Eighteen lakes were classified as high-sensitivity lakes and showed significant differences in latitude, surface area, elevation, dissolved calcium and magnesium concentrations, and conductivity compared to 25 low-sensitivity lakes. In high-sensitivity lakes, richness decreased on average by 6 species and body size decreased by 0.2 mm. This study presents a historical context for constructing effective conservation and management efforts at a time of substantial environmental change in low-nutrient NB lakes.