The Comite River originates in East and West Feliciana parishes in southeastern Louisiana, flowing southward through East Baton Rouge Parish before joining the Amite River just north of U.S. Route 190 between eastern Baton Rouge and Denham Springs. This slow-moving waterway winds through forested floodplains and bottomland hardwood forests, creating a protected corridor that supports diverse wildlife while serving critical flood management functions for the Baton Rouge metropolitan area.

A portion of the Comite holds Louisiana Scenic River designation, extending from Highway 10 west of Clinton downstream to where White Bayou enters the river south of Comite Drive. This designated stretch preserves the river's aesthetic and ecological values, protecting its relatively undisturbed character through conservation measures. The river corridor encompasses approximately 11,000 acres of protected wetlands, bottomland hardwood forests, and floodplain habitats that help mitigate flooding in this rapidly developing region.

Paddling opportunities concentrate in several well-established sections accessible through public conservation areas. The upper reaches between Highway 10 and Plank Road offer some of the finest paddling, characterized by beautiful scenery and minimal development. Further downstream, the stretch from Plank Road to Pride-Port Hudson Road continues this pattern of natural beauty with limited human impact. Public access points include Blackwater Conservation Area, which requires a half-mile carry on flat trails to reach the river, Waddill Wildlife Refuge (open Tuesday through Saturday with a 0.4-mile walk to the water), and Frenchtown Road Conservation Area with a two-thirds mile approach. These access points enable trips ranging from short excursions to full-day paddles, including a popular 7.25-mile run from Blackwater to Waddill and a ten-mile stretch from Blackwater to Frenchtown.

All sections feature flatwater conditions suitable for paddlers of varying experience levels, though the slow current requires some paddling effort. Water levels fluctuate significantly, with higher flows providing easier passage over sandbars while low water may necessitate portaging or careful route selection. The river supports healthy populations of largemouth bass, Kentucky bass, catfish, and various sunfish species, making it popular with anglers. Birdwatchers frequently observe herons, egrets, kingfishers, and migratory waterfowl along the corridor. The surrounding forests contain over 50 documented species of reptiles and amphibians, with cypress-tupelo breaks adding habitat diversity.

The Comite River Diversion Canal project, currently under construction, represents a major flood control initiative that will impact the lower river sections. Desnagging operations have removed fallen trees to improve flow during high water stages, particularly in areas north of the planned diversion canal exit point near Highway 64 east of Zachary.