Some streams in the watershed are impacted by nutrients, sediment, E. coli, and thermal radiation and one unnamed tributary is designated as an impaired waterbody.

Rapid Run is a freestone mountain stream in the ridge and valley physiographic province.

Rapid Run begins in a valley in Miles Township, Centre County.

It flows in a generally east-northeasterly direction for a few miles and receives the tributary Yankee Run from the left before entering Hartley Township, Union County.

In this township, the stream crosses Pennsylvania Route 192 and passes by a spring called The Little Bubbler.

[1] After more than a mile, Rapid Run enters Lewis Township, Union County.

Here it continues flowing east in its valley, alongside Pennsylvania Route 192 and Jones Mountain.

In West Buffalo Township, it continues heading east for more than a mile before crossing Pennsylvania Route 192 one last time and turning east-southeast.

The stream then leaves its narrow valley and flows alongside a much shallower, broader one that it shares with Stony Run.

[1] Rapid Run joins Buffalo Creek 10.22 miles (16.45 km) upstream of its mouth.

[2] A total of 4.1 miles (6.6 km) of tributaries to Rapid Run are designated as impaired waterbodies.

[3] At the point where the stream drains 3.50 square miles (9.1 km2), the average daily discharge is 6.59 cubic feet per second (0.187 m3/s).

Further downstream, where it drains 10.74 square miles (27.8 km2), its average daily discharge is 20.22 cubic feet per second (0.573 m3/s).

At the point where it drains 14.53 square miles (37.6 km2), the average daily discharge is 27.35 cubic feet per second (0.774 m3/s).

[3] The concentration of alkalinity in Rapid Run between Buffalo Trail and T-383 is 3 milligrams per litre (0.00019 lb/cu ft).

[9] In the water gap of Rapid Run, a number of sedimentary rock formations are exposed along Pennsylvania Route 192.

This ice-dammed lake was the largest in the area, with a volume of 0.973 cubic kilometers (0.233 cu mi).

However, in the distant past, a right-angle tributary of Rapid Run (which at the time was confined to the Fourteenmile Narrows) cut its way back from near Seven Notch Mountain and "beheaded" the upper reaches of Elk Creek, causing the headwaters of Elk Creek to flow into Rapid Run.

[8] The capture of the headwaters of Elk Creek by Rapid Run occurred approximately one million years ago and has been described as a "blatant act of 'stream piracy'".

[8] Aggradation at the mouth of the stream once partly dammed Buffalo Creek, resulting in as much as 98 feet (30 m) of fill.

The only part of the watershed where agricultural land is predominant is the area in the vicinity of the stream's impaired tributary.

[11] Daniel Reish of Berks County, Pennsylvania settled in the vicinity of Rapid Run in Forest Hill in 1820 and constructed a sawmill, gristmill, and distillery.

[14] The first stone dam ever built by the Civilian Conservation Corps impounds Halfway Lake on Rapid Run.

A bridge carrying Pennsylvania Route 192 over the stream was built 4 miles (6.4 km) north of Cowan in 1932 and repaired in 1987.

A two-span bridge carrying State Route 1002 was built over the stream 3 miles (4.8 km) west of Mazeppa in 1965.

In a 2008 report, the watershed of Rapid Run was ranked fifth amongst sub-watersheds in the Buffalo Creek drainage basin for restoration priority.

[16] Wild trout naturally reproduce in the stream from its headwaters downstream to its mouth.

[3] Additionally, a freshwater sponge known as Spongilla fragilis has been observed in the stream, but only near the Halfway Dam.

[3] Rapid Run has been described as a "high quality" stream with "excellent" angling opportunities.