Stony Brook starts in northwestern North Centre Township, on the southern edge of Knob Mountain.

The valley gets steeper as the stream turns south and then west, flowing north of Summer Hill.

The stream crosses Pennsylvania Route 487 and shortly reaches its confluence with Fishing Creek.

This rock formation consists of shale and has a high concentration of fossils, including two varieties of spirifier.

[6] The Columbia County Natural Heritage Inventory from 2004 designated the watershed of Stony Brook as a "locally significant site".

[10] In 2009, 25 local volunteers cleaned up of 17.15 tons of debris that had been left at the confluence of Stony Brook with Fishing Creek during a flood in June 2006.

Other trees inhabiting the valley include beech, basswood, two varieties of oak, yellow birch, black cherry, pignut hickory, tulip poplar, white ash, and sugar maple.

These include blue cohosh, false hellebore, twisted stalk, miterwort, golden saxifrage, barren strawberry, false Solomon's seal, Solomon's seal, Canada violet, purple trillium, wild stonecrop, trout lily, dwarf ginseng, and white baneberry.