More than 80 species of fish are found in the stream, including 15 species of darters—small, colorful perch-like fish that feed on small crustaceans, larvae and flies around and under rocks. Eight of the darter species are listed as threatened or endangered in Pennsylvania. Spotted Darters (Etheostoma maculatum) exist only in the French Creek and the Upper Allegheny River. Darters depend on clean, unpolluted water. Major threats to the fish are habitat alteration or loss, pollution, and competition from exotic species.

French Creek also supports healthy populations of smallmouth bass, walleyes, panfish, northern pike and muskellunge, species prized by sport anglers, and most of its tributaries are annually stocked with trout. The West Branch also supports the PA threatened mountain brook lamprey (Ichthyomyzon greeleyi) and Ohio lamprey (Ichthyomyzon bdellium).