Fishery surveys of rivers and streams too small to navigate by boat often ignore deep waters, however documenting seasonal fish species richness, composition, and abundance in these habitats could be important to a comprehensive understanding of fish community dynamics. We used a hand-drawn Siamese trawl to compare spatio-temporal patterns of fish assemblage structure in wadeable vs. non-wadeable habitats during spawning and post-spawning seasons at eight sites along a midstream reach of the Neosho River, Kansas, USA, a perennial, warmwater stream. Species composition varied modestly between wadeable and non-wadeable pools. Had deep waters not been sampled, some species would have been underrepresented in the community, including Ghost Shiner (Notropis buchanani), which was the most abundant fish in non-wadeable pools during both seasons. Others would have been missed entirely, such as large-bodied fishes like Shortnose Gar (Lepisosteus platostomus), Smallmouth Buffalo (Ictiobus bubalus), and White Crappie (Pomoxis annularis), which we captured only in non-wadeable pools, although these species were rare in our samples. A multivariate dispersion test indicated significant differences between seasons and among mesohabitats, with non-wadeable pools having more variability. These data suggest that characterization of fish community structure in warmwater rivers should include consideration of seasonality and deep, non-wadeable habitats.