Water resources dominate the landscape of Acadia National Park. Integral to ecosystem health and function, the waters of Acadia also allow visitors to engage in a variety of recreational pursuits, including fishing, sightseeing, canoeing, sailing, and swimming. Protection of the scientific and scenic attributes associated with Acadia's lakes, streams and wetlands, and their use as a source of public drinking water, were significant factors in the park's establishment. Water resources within or adjacent to Acadia include 14 Great Ponds (lakes greater than 4 hectares/10 acres), 10 smaller ponds, more than two dozen named streams and 10 named wetland areas. Lakes and ponds cover about 1,052 ha and wetlands cover about 1,670 ha, equivalent to approximately 7.4% and 10.1%, respectively of the park's area. Park staff have been monitoring Acadia's lakes and ponds since the early 1980's. The program is designed to document current conditions, to assess the effects of threats such as acid deposition and nutrient inputs, and to track long-term trends.

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 waterbodies less succeptable 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 souce 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.