Monitoring data collected since the early 1980's show that most of Acadia National Park's lakes and ponds have excellent water quality. Although most watersheds of Acadia lie at least partially outside the park boundary, the majority of upland portions are owned by the park. This makes many of the water bodies less susceptible to the effects of household, agricultural, and industrial non-point source pollution.

The effects of atmospheric deposition are another major concern at the park. Acid precipitation (rain, snow, and fog) can be a major influence on lake and stream chemistry, and can cause nutrient enrichment in estuaries. The major lakes and ponds of Acadia have near-neutral pH levels that appear to be relatively stable over time. The buffering capacities of park lakes are generally very low, making them potentially vulnerable to episodic acidification.

This condition occurs occasionally in some of the park's headwater streams. Recent studies discovered high concentrations of mercury in several freshwater fish species sampled in park lakes. The major source of mercury in lakes appears to be deposition from the atmosphere, and it then concentrates in the food chain. Consumption of mercury-contaminated fish can be harmful to humans as well as to other wildlife.