We examined why the lower Little Colorado River (LCR), Arizona continues to be dominated by four native fish species despite decades of encroachment by nine nonnative species. Most perennial flow begins at Blue Spring, located at river kilometer (RKM) 20.74 above the LCR's mouth, which is supplemented downriver by other springs. Blue Spring's water is extremely supersaturated with dissolved CO₂ (658 mg/L), and at baseflow the CO₂ concentrations apparently functioned as a fish-barrier for about 1 km further downriver until it outgassed to 288 mg/L. Thereafter, CO₂ outgassed to 202 mg/L by the top of Chute Falls (RKM 14.20) and 76 mg/L near the river's mouth. Chute Falls, and high CO₂ levels above it, obstruct upriver, but not downriver, fish movements; however, we still captured fishes from eight nonnative species above this falls. Our findings indicate most warmwater nonnative fishes in the LCR were immigrants from upriver sources within and bordering the intermittent corridor that invaded the system during floods, while most coldwater trout invaded from the Colorado River. Most nonnative species failed or were severely limited at reproducing progeny in the LCR, except occasionally by channel catfish Ictalurus punctatus and fathead minnow Pimephales promelas in the lower 13.57 km corridor, which was likely related to CO₂. Correlation tests suggested severe flood and/or suspended sediment regimes reduced populations of fathead minnows, red shiners Cyprinella lutrensis, and plains killifish Fundulus zebrinus in the LCR. Conversely, severe suspended sediment regimes (especially ≥60,000 mg/L) increased channel catfish, black bullhead Ameiurus melas, and common carp Cyprinus carpio, hypothetically by paralyzing these fishes upriver, whereby many drifted downstream and recovered in the lower LCR; however, their abundances decreased after prolonged periods of high CO₂. Nonnative fishes are controlled in the LCR by the system's endemic abiotic conditions.