Large‐bodied fish migration and residency in a flood basin of the Sacramento River,California, USA

River–floodplain complexes represent some of the most variable and diverse habitats on earth, yet they are among our planet's most threatened ecosystems. Use of these habitats by large‐bodied fishes is especially poorly understood, particularly in temperate regions. To provide insight into the factors that affect floodplain assemblages and migration, we sampled large‐bodied fishes with a fyke trap for 7 years in the Yolo Bypass, the primary flood basin of the Sacramento River, California. We collected a total of 18,336 individual fish comprised of 27 species, only 41% of which were native. Year‐round resident species white catfish Ameiurus catus, channel catfish Ictalurus punctatus and common carp Cyprinus carpio (all alien species) were the most abundant and comprised 74% of the total catch. Splittail Pogonichthys macrolepidotus (3.8%), white sturgeon Acipenser transmontanus (2.3%) and Sacramento sucker Catostomus occidentalis (1.1%) were the primary native species. We found that seasonal variation in water temperature and flood stage were important factors affecting the fish assemblage structure and the presence of migratory species. American shad Alosa sapidissima, an alien species, showed highest abundance during the early summer upstream migration, when temperatures were warmer. For native species, the abundances of white sturgeon, splittail, Sacramento pikeminnow Ptychocheilus grandis and Sacramento sucker were all highest during flood pulses. While our results suggest that flow alone is not sufficient to control alien species, the strong linkage between native fish migration and flow pulses highlights the importance of river–floodplain connectivity for the conservation of native fishes.