The creek's discharge averages 49 cubic feet per second (1.4 m3/s) at Sonestown, but can be up to a thousand times higher at Muncy.

Deep Hollow Run then enters the creek, which heads south away from the Laporte Township/Davidson Township border.

After several miles, it reaches the community of Sonestown, where the tributary Big Run flows into it from the north.

Muncy Creek then makes a sharp bend south and begins flowing parallel to U.S. Route 220.

After a few miles, it passes the community of Muncy Valley and makes a sharp turn south, exiting Davidson Township.

It continues following U.S. Route 220 during this time, picking up a few tributaries, including Lick Run.

Beyond the community, the creek continues south into Wolf Township, leaving its valley passing by the eastern edge of Hughesville.

Some distance further on, the creek receives the tributary Sugar Run and some miles later leaves Wolf Township in a southwesterly direction.

The creek then receives the tributary Wolf Run and immediately afterwards empties into the West Branch Susquehanna River.

[5] Muncy Creek joins the West Branch Susquehanna River is 27.88 miles (44.87 km) upstream of its mouth.

This stream reaches its confluence with Muncy Creek 0.06 miles (0.097 km) upstream of its mouth.

[9] The osmotic pressure of the stream's waters at this location ranged from less than 1 up to 4 millios-moles per 2.2 pounds (1.00 kg).

The water hardness of the creek (in terms of the concentration of calcium carbonate) ranges from 28 to 49 milligrams per liter (1.0×10−6 to 1.8×10−6 lb/cu in).

[8] There are trace amounts of bromides, phosphorus, orthophosphates, and ammonia in Muncy Creek.

[11] A narrow belt of the Chemung Formation occurs along Muncy Creek in Shrewsbury Township, Lycoming County.

[1] An outcropping of the Catskill Formation also occurs along parts of the creek in Jordan Township, Lycoming County.

Additionally, Beaver Lake (which has an area of 6 acres (2.4 ha)) is located in the watershed of the tributary Little Muncy creek.

[7] Communities in the watershed of Muncy Creek include Hugesville, Picture Rocks, Lairdsville, and Sonestown.

Smaller communities in the creek's watershed include Muncy Valley, Eagles Mere, and Nordmont.

[7] In the late 1800s, the only road in Davidson Township, Sullivan County besides the Susquehanna and Tioga Turnpike passed near Muncy Creek and the settlements along it.

[14] Additionally, six Native American lance heads made of stone were found near the creek by Joseph Fahrenbach in the autumn of 1872.

[18] Historically, railroads ran parallel to Muncy Creek 26 miles (42 km) upstream from its mouth, as far as the community of Nordmont.

[13] In the early 1900s, many of the sewers in the community of Eagles Mere discharged into tributaries of Muncy Creek, such as Outlet Run.

[11] Other major industries in the watershed in the early part of the 1900s included clay mines and furniture factories.

[7] From its headwaters to a point 26.4 miles (42.5 km) upstream of its mouth, the drainage basin of Muncy Creek is designated as Exceptional Value and a Migratory Fishery.

[20] A total of 92 percent of assessed streams in the watershed of Muncy Creek are inhabited by trout.

[15][22] There are some forested areas in the floodplains of Muncy Creek in the United States Geological Survey quadrangle of Hughesville.

He describes Muncy Creek as a "pleasing but generally mediocre mountain stream" in his book Keystone Canoeing.