The dynamic nature of large rivers is often diminished by anthropogenic alterations resulting in simplified stream networks with decreased floodplain connectivity and ecological function which adversely impact native organisms. However, little is known about the importance of large river floodplains to fish communities in the Pacific Northwest, especially during winter high flows. Our objectives were to document seasonal use of a Willamette River floodplain for native and non-native fish by measuring: 1) fish community characteristics (species richness, native versus non-native status, relative abundance), 2) spawning and rearing, 3) timing of use and movement, and 4) use by federally protected juvenile spring Chinook salmon (Oncorhynchus tshawytscha). During fall 2011 through spring 2012, a floodplain was sampled with a backpack electrofisher and out-migrant trap. A total of 12 native and 11 non-native species were detected. During nine electrofishing samples, 691 fish were collected, of which 95% were native. An estimated 42,297 fish were captured by the out-migrant trap; 98% of which were native and most were age-0 threespine stickleback (Gasterosteus aculeatus). Native species were detected on the floodplain prior to non-native species and tended to emigrate from the floodplain before non-native species, leading to a higher potential of stranding for non-native species as waters recedes. This study documents use of floodplain habitat by native and non-native fish species for seasonal flood refuge, rearing and spawning. Our results demonstrate native fish communities could potentially benefit from conservation of existing floodplains and restoration of floodplains changed by land use practices and altered flow regimes.