Tributaries of the Little Conemaugh River include Kokomo Run, Bear Rock Run, Noels Run, Bens Creek, Trout Run, North Branch, Laurel Run, South Fork, Saltlick Run, and Clapboard Run. Though most of the Little Conemaugh River main stem is still significantly impaired by abandoned mine drainage, some of the Watershed's tributaries support viable fisheries and trout stockings, the largest of which is the North Branch. Though many abandoned mine discharges continue to spew pollution into the River, Hughes Borehole, the Miller Shaft and the Sonman Shaft provide, by far, the largest negative impact, contributing about 7,000 gallons of pollution to the Little Conemaugh River every minute! The challenges of Little Conemaugh River restoration are complex, but the Little Conemaugh and Trout Run Watershed Associations, along with other partners, are working to clean up its pollution.

Kokomo Run

Kokomo Run, which also drains the Cresson Wetlands, brings water from two significant abandoned mine discharges into the river.

Bear Rock Run

Bear Rock Run is a tributary that originates on the west slope of the Allegheny Front and is impacted by drainage from an abandoned clay mine. A reclamation project on Bear Rock Run has improved its water quality and is owned by the Cambria County Conservation & Recreation Authority.

Hughes Borehole

Hughes Borehole discharges from 800 to 3,500 gallons of acidic mine water each minute, which enters the river near Lilly, effectively destroying fish life. The borehole causes a spectacular wasteland of more than five acres with a moonscape of iron oxide in dramatic colors of red, orange and yellow crossed by a ribbon of bright green, acid-loving algae.

Noels Creek and Bens Creek

Noels Creek and Bens Creek bring good water to the Little Conemaugh from the north and southeast, respectively, just upstream of Portage. But, their positive effects are soon erased by two large and one moderate mine discharge totaling 1,752 gallons a minute and dropping more than 10,000 pounds of metals per day into the river.

Trout Run

Trout Run carries pollution from several small discharges and one large one – the Miller Shaft discharge, which contributes more than 14,000 pounds of metals per day, about 13 percent of the Little Conemaugh’s entire pollution load. A 100 gallon per minute discharge is now being treated from the old Puritan Mine with a passive wetland system.

The North Branch of the Little Conemaugh

The North Branch of the Little Conemaugh is large tributary, draining 31 square miles. It improves the quality of the river, as it and its tributaries support stocked trout fisheries. The North Branch begins north of Ebensburg and its watershed includes Lake Rowena, a 15-acre reservoir. The North Branch also supports the Wilmore Reservoir, an industrial water supply now owned by the Cambria Somerset Authority and open to the public. The North Branch enters the Little Conemaugh at Wilmore.

Laurel Run

Laurel Run brings good water and a pH exceeding 7 to the Little Conemaugh. But, it is a small stream that has little effect on the river.

Main Stem

At Ehrenfeld, a mine-drainage treatment plant discharges at least 4,700 gallons a minute of high alkalinity water into the river. The high volume of water has a significant effect on the Little Conemaugh’s water quality. So does another discharge that enters at Ehrenfeld, as does runoff from a 67 acre coal refuse pile there. Together, they contribute about 12 percent of the river’s pollution load.

The South Fork of the Little Conemaugh

The South Fork of the Little Conemaugh meets the main stem about 5 miles below the mouth of the North Branch, draining 64 square miles. It’s headwaters on the Allegheny Front above Beaverdale and Dunlo support wild brook trout and the Beaverdam Run Reservoir, one of the largest bodies of water in the area and open to the public. The South Fork was once famous for its trout fishing, but pollution killed them off long ago. Now, it is notorious for the collapse of the South Fork Dam, which caused the Johnstown Flood of 1889. The South Fork is heavily polluted. The St. Michael (or Topper Run) Discharge flows at about 4,000 gallons a minute and contributed 29 percent of the Little Conemaugh’s pollution load but is now treated actively by Rosebud Mining Company. Sulfur Creek and Otto Run in the Sidman area also bring significantly polluted water from several discharges to the South Fork.

Saltlick Run

Saltlick Run enters in Mineral Point. It is a fairly small tributary that both feeds and drains the Saltlick Reservoir, a potable water supply impoundment. Saltlick Run has naturally reproducing brook trout in its headwaters above the reservoir, where mine discharges were long piped to a point below the dam to preserve the water quality. A recently completed remediation project now treats one of those discharges above the dam.

Clapboard Run

Clapboard Run carries mine drainage through Franklin and joins the Little Conemaugh as it reaches the outskirts of Johnstown.

The Conemaugh River

The Conemaugh River begins at The Point in downtown Johnstown where the Little Conemaugh joins the Stonycreek. The difference in water quality between the two rivers is obvious here, where the Stonycreek’s cleaner waters stand in stark contrast to the iron-laden, murky flow of the Little Conemaugh. Although long thought to be dead beyond hope, the Conemaugh River supports a growing though marginal sport fishery at several areas from Seward downstream. Hinckston Run enters from the north and supports a stocked trout fishery in its headwaters. Below the Hinckston Run Dam, another former industrial waste site causes significant degradation to the stream. This dam is another water supply owned by the Cambria Somerset Authority and open to the public. Laurel Run is another small tributary that enters from the north and supports a fishery. Gray Run enters from the south through Johnstown's West End. There is a small passive treatment system on it, owned by the Cambria County Conservation & Recreation Authority.