We used histological features to identify the spawning chronologies of river-dwelling populations of slenderhead darter Percina phoxocephala, suckermouth minnow Phenacobius mirabilis, stonecat Noturus flavus, and red shiner Cyprinella lutrensis and to relate their reproductive status to microhabitat associations. We identified spawning and nonspawning differences in habitat associations resulting from I year of field data via logistic regression modeling and identified shifts in microhabitat selection via frequency-of-use and availability histograms. Each species demonstrated different habitat associations between spawning and nonspawning periods. The peak spawning period for slenderhead darters was April to May in high-velocity microhabitats containing cobble. Individuals were associated with similar microhabitats during the postspawn summer and began migrating to deeper habitats in the fall. Most suckermouth minnow spawned from late March through early May in shallow microhabitats. The probability of the presence of these fish in shallow habitats declined postspawn, as fish apparently shifted to deeper habitats. Stonecats conducted prespawn activities in nearshore microhabitats containing large substrates but probably moved to deeper habitats during summer to spawn. Microhabitats with shallow depths containing cobble were associated with the presence of spawning red shiners during the summer. Prespawn fish selected low-velocity microhabitats during the spring, whereas postspawn fish selected habitats similar to the spawning habitat but added a shallow depth component. Hydraulic variables had the most influence on microhabitat models for all of these species, emphasizing the importance of flow in habitat selection by river-dwelling fishes. Histological analyses allowed us to more precisely document the time periods when habitat use is critical to species success. Without evidence demonstrating the functional mechanisms behind habitat associations, protective flows implemented for habitat protection are unlikely to be effective. ?? Copyright by the American Fisheries Society 2006.