The Susquehanna River Basin Commission said the overall health of the river basin is improving, but there are some problem areas.
The commission said important data on the 49,000 miles of rivers and streams in the basin comes from a network of gauges, but funding for many of those was lost in 2011. The gauges are used to monitor water and pollutant levels.
Paul Swartz, the commission's executive director, said in a statement that "we would literally be flying blind" without the stream gauge data.
More than 2,000 miles of streams are polluted by mine drainage, and smallmouth bass in the lower region are suffering from increasing levels of disease, Swartz said. The cause of that isn't known. Drinking water protection is also a concern in some areas, he said.
Throughout the basin 32 percent of rivers and streams have water quality that isn't impaired, 40 percent are slightly impaired, 23 percent are moderately impaired, and 5 percent are severely impaired, the report said. Between 2010 and 2012 the number of stream miles that were polluted by stormwater runoff rose from 1,120 to 1,150.
However, the report said that the main branch of the river meets or exceeds standards along most of its 444 miles, and many smaller watersheds are pristine.
Total water use in the basin is increasing, too.
Electric power companies were by far the largest user, withdrawing 86.4 million gallons of water per day in 2010, and 92.7 million gallons per day in 2012. Water use by the natural gas industry also rose significantly, from 1.3 million gallons per day in 2010 to 10.4 million gallons per day in 2012.
Public water supplies used 8.9 million gallons per day in 2012, down slightly from 2010.
The Susquehanna basin flows 444 miles from headwaters in Cooperstown, N.Y. to Havre de Grace, Maryland.