During 1998 and 1999, larval fish phenology, abundance, and diversity were characterized at 13 reaches in the Buffalo River and Sand Hill River, tributaries of the Red River of the North. Channelized reaches were less stable than unchannelized reaches, showing more overall variation and greater daily fluctuation in temperature and dissolved oxygen (DO), and a higher level of intermittent flow. These reaches also exhibited significantly lower larval diversity. Principal component analysis explained > 84% of the variance for the first two axes for larval catch, with axis 1 associated with channelization and axis 2 associated with temperature and DO. Fathead minnow (Pimephales promelas) was associated with channelized reaches, whereas spotfin shiner (Cyprinella spiloptera), common shiner (Luxilis cornutus), redhorse (Moxostoma spp.), and darters (Etheostoma spp.) were associated with unchannelized reaches in both years. Clear associations of reproductive guilds with channel type were not detected, but species of intermediate pollution tolerance were associated with unchannelized reaches and tolerant species were associated with channelized reaches.