Freshwater lakes in the Canadian Maritime provinces have been detrimentally influenced by multiple, often synergistic, anthropogenically-sourced environmental stressors. These include surface-water acidification (and a subsequent decrease in calcium loading to lakes); increased nutrient inputs; watershed development; invasive species; and climate change. While detailed studies of these stressors are often hindered by a lack of predisturbance monitoring information; in many cases, these missing data can be determined using paleolimnological techniques, along with inferences on the full extent of environmental change (and natural variability), the timing of changes, and linkages to probable causes for change. As freshwater resources are important for fisheries, agriculture, municipal drinking water, and recreational activities, among others, understanding long-term ecological changes in response to anthropogenic stressors is critical. To assess the impacts of the major water-quality issues facing freshwater resources in this ecologically significant region, a large number of paleolimnological studies have recently been conducted in Nova Scotia and southern New Brunswick. These studies showed that several lakes in southwestern Nova Scotia, especially those in Kejimkujik National Park, have undergone surface-water acidification (mean decline of 0.5 pH units) in response to local-source SO2 emissions and the long-range transport of airborne pollutants. There has been no measureable chemical or biological recovery since emission restrictions were enacted. Lakewater calcium (Ca) decline, a recently recognized environmental stressor that is inextricably linked to acidification, has negatively affected the keystone zooplankter Daphnia in at least two lakes in Nova Scotia (and likely more), with critical implications for aquatic food webs. A consistent pattern of increasing planktonic diatoms and scaled chrysophytes was observed in lakes across Nova Scotia and New Brunswick, suggesting that the strength and duration of lake thermal stratification has increased since pre-industrial times in response to warming temperatures (∼1.5 °C since 1870). These include three lakes near Bridgewater, Nova Scotia, that are among the last known habitat for critically endangered Atlantic whitefish (Coregonus huntsmani). Overall, these studies suggest that aquatic ecosystems in the Maritime Provinces are being affected by multiple anthropogenic stressors and paleolimnology can be effective for inferring the ecological implications of these stressors.