Fish-habitat associations in streams have been widely studied; however, temporal considerations have been neglected, particularly during the winter. We quantitatively sampled perennial headwater streams in the Missouri Ozarks during the summer (n = 13) and winter (n = 4) to evaluate possible habitat shifts by three benthic fishes at two spatial scales: channel unit and microhabitat. Density of all three headwater species in streams was generally lower in winter than summer, with some species being ubiquitous in channel units of streams during the summer and almost entirely absent from the same streams during winter. Presence of each of three species during the summer varied by stream and channel unit, but patterns of channelunit use did not change depending on stream sampled. Ozark sculpin (Cottus hypselurus) was more likely to be present (> 50% probability) in riffles and runs, but not pools. Fantail darter (Etheostoma flabellare) was much more likely to be found in riffles than other channel units whereas rainbow darter (Etheostoma caeruleum) was more likely to occur in runs or pools than riffles. During winter, each of the three species was equally likely to be present or absent from any of the channel units indicating a more general use of channel units. However, each of the three species used deeper microhabitats within pools and slower-velocity areas of riffles during winter compared to summer. Results of this study indicate benthic, headwater species used habitat more generally during cold-water periods compared to warm-water periods, but density estimates indicated changes in channel unit use occurred in some streams and patterns of fine-scale microhabitat shifts did occur.