Pennsylvania’s latest water quality report has found that 40% of its 85,000 miles of streams and rivers are violating the state’s water quality standards in some way, with agricultural runoff and acid mine drainage mostly to blame.An eroding stream winds through a farm field in Lancaster County, PA. Pennsylvania is targeting streams on farms where a lack of fencing to keep livestock out of the streams and little or no streamside vegetation sends nutrient pollution to local waters and the Chesapeake Bay. (PA Department of Environmental Protection)

That includes a stretch of the Susquehanna River, which flows into the Chesapeake Bay and has a major impact on the Bay’s health. The 46-mile segment of the middle and lower river, which has been plagued with sick fish in recent years, was found to be impaired for aquatic life because of high pH levels.

The draft 2018 Integrated Water Quality Monitoring and Assessment Report was released in May for public comment before submission of the final report to the U.S. Environmental Protection Agency.

The state also recently released a draft plan for meeting its share of the Chesapeake Bay cleanup goals, outlining the need to invest $485 million a year — more than twice what it is currently spending.

While that would help address some of the issues identified in the new water quality report, the state would need to spend significantly more to fix all of its stream health problems.

Not surprisingly, agricultural runoff of soil, nutrients and chemicals are the cause of the most miles of impaired waterways across the state — 5,741 in all. High concentrations of nutrients cause algae blooms in the Bay, reducing oxygen needed by aquatic life. Those blooms, along with sediment washed into the Bay, also block sunlight from reaching underwater grasses. And sediment can bury emerging grasses.

The amount of waterways impacted by agricultural runoff is actually 680 miles fewer than the last water quality assessment in 2016. On the surface, that appears to be an encouraging and logical trend because the amount of nutrients and sediment flowing down the Susquehanna into the Bay has been declining somewhat for years.

But the decline described in the report may be partly due to more accurate stream assessments rather than a direct result of stream improvements, said Dustin Shull, environmental group manager for the Pennsylvania Department of Environmental Protection.

The second-largest source of poor water quality was runoff from abandoned mines. When water draining from the old mines flows over exposed sulfur-bearing rock and materials, it becomes highly acidic. When flowing into streams, the mix kills or restricts aquatic life. The state reported that 5,575 miles of waterways are impacted by such runoff, a slight reduction from 2016.

Stormwater runoff, the third major source of pollution, picks up fertilizers, soil, pesticides and other contaminants and flushes them into streams. The amount of impacted waterways was 3,066 miles, up by 164 from 2016. Again, Shull said the figures may not mean a worsening of the problem but rather better assessment methods.

Pennsylvania, like every state, has to evaluate the water quality of its streams and rivers every two years to see if they meet water standards designed to protect such things as aquatic life, water supply, fish consumption and recreation. States submit the reports to the EPA, including a list of waterways that should be officially designated as “impaired.” The EPA reviews and approves the list, and the state must then develop plans showing how they will clean up those waterways.

For the first time, Pennsylvania’s 2018 report gauged the health of aquatic life on the lower and middle sections of the Susquehanna River and the Juniata River, a major tributary.

All wadeable streams in the state had been assessed for aquatic use previously but this was the first time that sections of the Susquehanna and Juniata were assessed.

The sections of both rivers were found to be impaired because of poor results for aquatic insects that are an important part of the food web and for high pH levels, a violation of water-quality standards.

The section of the Susquehanna now considered impaired for aquatic life runs from the mouth of the Juniata River at Duncannon downriver to Columbia, in Lancaster County.

If the EPA approves the report, the state will have to develop a cleanup plan for both sections of the rivers. The report does not identify a cause for the impairments, which will be required before a cleanup plan is made. But it notes that high pH levels are often tied to algae growth from high levels of nutrients, and Bay cleanup plans target nutrient reductions. Shull noted that there was evidence of algal blooms.

A 4-mile section of the Susquehanna was listed as impaired for recreation, as it was in the 2016 report, mainly for the presence of fecal coliform. The cause was not listed but sources could be manure from livestock, sewage treatment plants or industries.

The increased focus on the mainstem of the Susquehanna and Juniata has been driven by an alarming die-off of prized smallmouth bass beginning in 2005. About a year ago, scientists identified the cause as manmade chemicals, largely from ag-related herbicide runoff and reproduction-altering pharmaceuticals, as well as a virus and parasites.

The Pennsylvania Fish and Boat Commission has repeatedly requested that the state declare the lower Susquehanna impaired, which would require the state to come up with a plan to identify water-quality problems and fix them. But the administrations of two governors refused, instead launching detailed monitoring of the river.

Ironically, the bass have recovered to near-record levels in recent years while the Susquehanna has come under closer scrutiny and has now, indeed, been listed as impaired.

“DEP should have addressed this in 2005, when we had a major fish kill, but they’re finally taking the first step in admitting there’s a problem,” John Arway, the now-retired executive director of the Fish and Boat Commission told Pennsylvania Outdoor News.

The unprecedented sampling of the Susquehanna also has found troubling levels of “contaminants of emerging concern” — a group of pollutants that include hormones, pharmaceuticals and certain pesticides. The findings also have contributed to Pennsylvania initiating a statewide search for the cancer-causing group of chemicals known as PFAS that has been generating concerns nationwide.

As far as required cleanups of impaired waterways in the state, there is a clear priority by state environmental officials to address streams and rivers that drain into the Chesapeake Bay. About half of the state does.

“We’re telling the public that Pennsylvania DEP is focusing on agricultural impairments right now as a priority to restore,” Shull said.

One visible sign of that initiative is the creation of 28 “restoration priority watersheds.” All but three are in the Chesapeake Bay drainage and all but two are impaired because of agriculture runoff. “These are the places where we need to have our most restoration successes,” Shull observed.

The full report and supporting documents may be found online at The site includes, for the first time, an online interactive map where users can click on any stream in the state, see if it is impaired and, if so, the reasons for the problems.