Flora and fauna
Most of the Rogue River watershed is in the Klamath Mountains ecoregion designated by the EPA, although part of the upper basin is in the Cascades ecoregion, and part of the lower basin is in the Coast Range ecoregion. Temperate coniferous forests dominate much of the basin. The upper basin, in the High Cascades and Western Cascades, is in places "identified as containing extremely high species richness within many groups of plants and animals". Common tree species in the forests along the upper Rogue include incense cedar, white fir, and Shasta red fir.
Jeffrey pine is among tree species that thrive in serpentine soils.
Further downstream a diverse mix of conifers, broadleaf evergreens, and deciduous trees and shrubs grow in parts of the basin. In more populated areas, orchards, cropland, and pastureland have largely replaced the original vegetation, although remnants of oak savanna, prairie vegetation, and seasonal ponds survive at Table Rocks north of Medford. Oak woodlands, grassland savanna, ponderosa pine, and Douglas-fir thrive in the relatively dry foothills east of Medford; areas in the foothills of the Illinois Valley support Douglas-fir, madrone, and incense cedar. Parts of the Illinois River watershed have sparse vegetation including Jeffrey pine and oak and ceanothus species that grow in serpentine soils. The Klamath-Siskiyou region of northern California and southwestern Oregon, including parts of the southwestern Rogue basin, is among the four most diverse temperate coniferous forests in the world. Considered one of the global centers of biodiversity, it contains about 3,500 different plant species. The Klamath-Siskiyou region is one of seven International Union for Conservation of Nature (IUCN) areas of global botanical significance in North America and has been proposed as a World Heritage Site and UNESCO Biosphere Reserve.
The lower Rogue passes through the Southern Oregon Coast Range, where forests include Douglas-fir, western hemlock, tanoak, Port Orford cedar, and western redcedar, and at lower elevations Sitka spruce. Coastal forests extending from British Columbia in the north to Oregon (and the Rogue) in the south are "some of the most productive in the world". The coastal region, where it has not been altered by humans, abounds with ferns, lichens, mosses, and herbs, as well as conifers.
The Rogue River contains "extremely high-quality salmonid habitat and has one of the finest salmonid fisheries in the west. However, most stocks are less abundant than they were historically... ". Salmonids found in the Rogue River downstream of Lost Creek Lake include Coho salmon, spring and fall Chinook salmon, and summer and winter steelhead. Other native species of freshwater fish found in the watershed include coastal cutthroat trout, Pacific lamprey, green sturgeon, white sturgeon, Klamath smallscale sucker, speckled dace, prickly sculpin, and riffle sculpin. Nonnative species include redside shiner, largemouth bass, smallmouth bass, black crappie, bluegill, catfish, brown bullhead, yellow perch, carp, goldfish, American shad, Umpqua pikeminnow, and species of trout. Coho salmon in the watershed belong to an Evolutionarily Significant Unit (ESU) that was listed by the National Marine Fisheries Service as a threatened species in 1997 and reaffirmed as threatened in 2005. The state of Oregon in 2005 listed Rogue spring Chinook salmon as potentially at risk.
Trees and shrubs growing in the riparian zones along the Rogue River include willows, red alder, white alder, black cottonwood, and Oregon ash. A few of the common animal and bird species seen along the river are American black bear, North American river otter, black-tailed deer, bald eagle, osprey, great blue heron, water ouzel, and Canada goose.