Invasive crayfish have been shown to have negative impacts on a range of taxa, though the mechanisms for those effects have not always been evaluated. Signal crayfish (Pacifastacus leniusculus) in Sagehen Creek were associated with reduced growth rates and gut fullness of Paiute sculpin (Cottus beldingi) in earlier experiments. This paper assesses potential behavioral mechanisms of competition between the two species. I conducted experiments to determine crayfish effects on sculpin behavior and habitat use in a stream observation facility at the Sagehen Research Station, California, USA. Sculpin reduced their use of refuges and pools, shifted into higher-velocity microhabitats, and spent more time fleeing in the presence of crayfish. Crayfish used refuges, pools, and low-velocity habitats more than sculpin in either treatment. Both species were notably nocturnal, with most activity at dusk and night observations, although crayfish were more strongly so than sculpin. Detailed field surveys of lower Sagehen Creek found that potential refuges (unembedded rocks) were closely associated with total crayfish and sculpin numbers, suggesting that cover is at least sometimes limiting under natural conditions. By displacing sculpin from refuges and pools and increasing their activity rate, crayfish may increase the likelihood of predation on sculpin. Behavioral shifts in sculpin appear to be at least partly responsible for the reduced growth rates of sculpin in the presence of crayfish.