The Cispus River originates in the high glacial valleys of the Goat Rocks Wilderness within the Gifford Pinchot National Forest, flowing approximately 54 miles through Lewis and extreme northeast Skamania counties before joining the Cowlitz River at Lake Scanewa. Beginning near Snowgrass Flats at elevations exceeding 5,000 feet, the river follows a looped, southwesterly course through heavily forested terrain, draining much of south-central and southeastern Lewis County.

Major tributaries significantly shape the Cispus character. About 40 miles from its mouth, Muddy Fork enters from the left, carrying glacial debris from Mount Adams' Lava Glacier that gives the water its characteristic turbid appearance. Canyon Creek, originating high on Mount Adams' slopes, contributes substantial volume, as does the North Fork Cispus, which joins the main stem about 20 miles from the headwaters. Yellowjacket and McCoy Creeks enter from the south in the middle reaches, while Walupt Creek feeds the upper watershed.

The river corridor bears evidence of the early 20th-century Cispus Burn, which consumed most of the lower drainage's original forest. Regrowth now includes Douglas fir stands with trees reaching 600 years old in certain areas near Randle, alongside alder, cedar, hemlock, and maple. The watershed contains hundreds of culturally modified "basket trees" where indigenous peoples harvested bark for container-making.

Archaeological sites, including the Yuyutla location near Randle and Layser Cave, document thousands of years of use by the Upper Cowlitz (cispaclama) and other Native groups for tool-making, hunting, and seasonal camps. Tower Rock, a prominent quartz diorite monolith, marks a distinctive landmark along the southern bank in the middle reaches.

Downstream, the river transitions from Gifford Pinchot National Forest into the Weyerhaeuser Cowlitz Tree Farm before reaching its terminus at Lake Scanewa, just upstream from Cowlitz Falls and the flooded townsite of Kosmos.

Access to the upper river follows Highway 12 to Randle, then State Route 131 south to Forest Road 23, with Forest Road 21 paralleling much of the upper watershed. The Lewis County PUD kayak launch, marked with posted signs approximately 1.5 miles upstream from the Cowlitz confluence, serves as the official river mouth boundary. Cowlitz Falls Park provides day-use facilities near the confluence.

Fishing opportunities include brook trout in the upper reaches, with best conditions during summer and fall. A USGS stream flow monitoring station provides real-time data. The river supports whitewater rafting in certain sections, though specific run details vary with seasonal flows and forest access conditions.