We studied the effects of three flow regimes on the activity patterns and movements of one-, three-, six-, and 36-week old Colorado pikeminnows (Ptychocheilus lucius) and two-week old razorback suckers (Xyrauchen texanus) in an experimental tank under light and dark conditions. The seven-chambered tank simulated a system of backwater habitats, which are used by the young fishes in nature. Water flows through the tank were slow, and velocities were discernable only in the vicinity of surface ports that connected each chamber. Fish movements were related to light or dark condition and activity tended to increase with age. Larvae, relatively active in daylight, moved little at night with no flow, but flow stimulated night activity and downstream movement. Older fish also had a diminished response to flow direction during daylight, but responded at night. The tendency for night movement may be a predator avoidance mechanism, but the tendency to move downstream with flow is likely a response to life in backwater habitat. With inflow and backwater filling “downstream” larval movements would access expanding habitat. With outflow and backwater draining, downstream movement would avoid stranding and potential death in a shrinking habitat.