Increasing emphasis has been placed on reducing runoff from feedlots to protect the Chesapeake and other waterways, but Pennsylvania is moving to rein in another type of animal pollution: fish manure.

The Pennsylvania Department of Environmental Protection in February withdrew a draft discharge permit for one of the state’s largest trout hatcheries, which it blames for turning Big Spring Creek, a state-designated “exceptional value” stream, into an impaired waterway.

“Our studies proved the discharges were degrading the stream,” said Karen Sitler, a DEP spokeswoman. “The trout used to reproduce in that stream, but it appears they only reproduce above the discharge at this time.”

Now, the agency wants the Pennsylvania Fish and Boat Commission to find a way to minimize or end discharges from its Big Spring Fish Culture Station — and then consider using that technology at other hatcheries throughout the state.

If that happens, it could not only clean up local streams, but also halt the flow of huge amounts of nitrogen into the Bay each year.

The commission has nine trout hatcheries, seven of which are in the Bay watershed. Like feedlots, the hatcheries rear huge numbers of fish in a confined space, resulting in a buildup of waste.

Unlike some hatchery fish that are released as juveniles, most trout are raised until they become adults, when they are released just before the the opening of trout season. As the fish get big, they produce more waste, which results in increased sediment and nutrient discharges.

Estimates from the Bay Program indicate that state hatcheries in Pennsylvania’s portion of the watershed release more than 200,000 pounds of nitrogen a year — equivalent to the runoff from 14,500 acres of crop land. Exact figures for the Big Spring facility were not available, but it is one of the largest trout hatcheries, producing more than 700,000 adult, and 60,000 fingerling trout for stocking this year.

“We’re a big contributor, unfortunately,” acknowledged Dan Tredinnick, a spokesman for the commission.

Tredinnick said the hatcheries — including Big Spring — consistently operated within the conditions set in their discharge permits. Still, he said, the commission recognized its hatchery system needed statewide improvements even before the Big Spring controversy and has been working on a plan to slash discharges 25 percent statewide.

“We’re a natural resource agency,” he said. “Although we are in compliance with our discharge permits, being in compliance isn’t necessarily enough. We should, as a natural resource agency, be a leader. The permits set a minimum, and we think we should be doing better than that.”

Already, the commission is planning to cut trout production from 5.3 million this year to 4.5 million next year to reduce discharges. “Obviously, if you have fewer fish on station, you have less waste to treat, and you can treat it better and you are discharging less,” Tredinnick said.

In addition, the commission plans to explore using high-protein feed that would promote fish growth while producing less waste. It is also planning infrastructure improvements for its treatment of wastewater. But the upgrades will cost about $25 million, and Tredinnick said the commission — an independent agency that traditionally does not get general fund tax dollars to support its programs — would need financial support from the state to complete the work.

Tredinnick said the commission had already been planning changes at its Big Spring facility, including reduced production, feed changes and $2 million in upgrades that would reduce discharges 90 percent. But, he said, commission officials were not sure that its economically possible to totally eliminate discharges at Big Spring, as DEP suggested.

The Big Spring issue erupted last fall when the DEP issued a new draft permit for the Cumberland County-based hatchery. “There was a public outcry,” Sitler said.

Fishermen blamed the hatchery for the destruction of the stream’s natural brook trout population, which decades ago had a national reputation for luring anglers to the remote waterway. Many demanded the hatchery be closed immediately.

In the face of the protests, the DEP withdrew the draft permit and instead sent a letter to the commission saying the hatchery was “significantly degrading” the creek and that “it may take discontinuing the discharge entirely to ensure that the existing designated uses of Big Spring Creek are restored.”

Big Spring Creek, which is 5.1 miles long, is listed as an impaired waterway because of siltation, low dissolved oxygen and excessive nutrients. The stream is particularly susceptible to water quality problems because it is slower flowing than most trout streams, giving nutrients a better chance to spur algae growth, which sucks oxygen from the water.

The commission acknowledges that the hatchery is partly to blame for the stream’s condition, but contends that runoff from farms and developments in the area are also to blame. Also, misguided efforts by some people dating to the 1950s to “improve” the stream by clearing vegetation from the shoreline damaged important fish habitat.

Further, the commission contends that the creek’s water quality and fish population were degraded before it opened its hatchery in 1972, partly because of earlier commercial hatcheries that operated on the stream. Those commercial hatcheries also stocked nonnative brown and rainbow trout, both of which are more tolerant of reduced water quality than native brook trout. Both also outcompete brook trout in the same habitat.

While Big Spring supported a significant brook trout fishery until at least the 1940s, the commission says brook trout were on the wane before it built its hatchery. The commission’s hatchery stocks brook, brown and rainbow trout.

Tredinnick said the commission was concerned about the apparent intent of the DEP letter to restore a reproducing brook trout population in the stream. That, he said, could mean dealing with non-water issues such as trying to physically remove the competing brown and rainbow trout from the stream.

A DEP official later indicated the agency was concerned about the restoration of a reproducing cold-water trout fishery, and not exclusively brook trout.

The commission has until late April to respond to the DEP’s letter.

Both agencies do agree on one thing — they’ve teamed up to support the creation of a new watershed group that will seek state grants for restoration activities along Big Spring Creek.