The EPA reports that ecosystems harmed by acid rain deposition can take a long time to fully recover even after harmful emissions cease. The most chronic aquatic problems can take years to be resolved. Forest health is even slower to improve following decreases in emissions, taking decades to recover from damage by acid deposition. Finally, soil nutrient reserves (such as calcium) can take centuries to replenish.

According to the USGS in Trends in Precipitation Chemistry in the United States, 1983–1994: An Analysis of the Effects in 1995 of Phase 1 of the Clean Air Act Amendments of 1990, Title IV, rainwater tested at 109 test sites across the United States was less acidic in 1995 than in 1983, particularly along the Ohio River Valley and in the Mid-Atlantic region. SO₅ had declined at 92 percent of the sites. The USGS attributed the improvement to the standards put in place by the Clean Air Act Amendments Title IV program. For nitrates, approximately as many sites showed decreased levels as reported increased levels. Overall, nitrate levels rose slightly, with the largest increases occurring in the western states.

In April 1999 NAPAP released findings from the study National Acid Precipitation Assessment Program Biennial Report to Congress: An Integrated Assessment. The study warned that, despite important strides in reducing air pollution, acid rain remained a serious problem in sensitive areas. The report provided additional evidence that acid rain is more "complex and intractable than was believed 10 years ago." Among the findings were the following:

• New York's Adirondack Mountain waterways suffer from serious levels of acid. Even though sulfur levels are declining, nitrogen levels there are climbing. The agency predicted that by 2040 about half the region's 2,800 lakes and ponds will be too acidic to sustain life.
• The Chesapeake Bay is suffering from excess nitrogen, which is causing algae blooms that suffocate other life forms.
• High elevation forests in Colorado, West Virginia, Tennessee, and southern California are nearly saturated with nitrogen, a key ingredient in acid rain.
• High elevation lakes and streams in the Sierra Nevadas, the Cascades, and the Rocky Mountains may be on the verge of "chronically high acidity."

The report concluded that further reductions in sulfur and nitrogen would be needed. The report also found, however, that the 1990 Clean Air Act Amendments have reduced sulfur emissions and acid rain in much of the United States. Some scientists believe that the problems associated with acid rain are theoretically reversible. That is, recovery is possible if a threshold of damage is not passed.

In March 2000 the EPA and the U.S. General Accounting Office (GAO) concluded in Acid Rain: Emissions Trends and Effects in the Eastern United States that some surface waters in New England harmed by acid rain were showing signs of recovery. However, ecosystems considered most severely affected—such as the Adirondacks—were not yet showing improvement. The GAO reported that acidified lakes in the Adirondack Mountains were taking longer to recover than lakes elsewhere and might not recover fully or at all without further reductions in acid deposition. Recovery was considered dependent on improving the nearby soil condition.

In early 2001 the EPA released a report on progress made by the United States and Canada on cross-border air pollution. The study, U.S.-Canada 2000 Air Quality Agreement Progress Report, is the fifth biennial report related to the 1991 agreement between the two countries. The report says that SO₅ deposition was reduced by up to 25 percent between 1995 and 1998 over a large area of the eastern United States. Most of the reduction was in the Northeast, where many sensitive ecosystems are located. SO₅ concentrations in lakes and streams decreased all over North America. Declines in nitrate concentrations were much smaller and rarer. Only one region, Vermont/Quebec, showed recovery as evidenced by decreasing acidity or increasing alkalinity.

In 2001 the Hubbard Brook Research Foundation released Acid Rain Revisited, which examined progress since 1990. The report concluded that acid rain was still a significant problem in the Northeast, despite declines in sulfur emissions. Researchers urged for tighter controls on emissions of NO₅ and ammonia, two problems that have not been well addressed by the Acid Rain Program.

The report noted that many ecosystems in the northeast have reached or passed their tolerance for acid input, making recovery unlikely under the existing emissions reductions scheme. The researchers called for an additional 40 to 80 percent reduction in sulfur emission from electric utilities in addition to what is mandated now. Reductions at the 80 percent level are predicted to allow recovery of acidic streams to nonacidic status in approximately 20 to 25 years.