Major declines in biodiversity are occurring globally, and data for native and non-native fish assemblages in freshwaters, especially large rivers, are limited. We assessed assemblages of native and non-native fishes of the mainstem Willamette River, Oregon in 2011-2013 and 2021-2023, as well as three major tributaries in 2015-2017, using consistent boat and backpack electrofishing methods. The Willamette River basin contains 34 species of native fish and 30 non-native species; the mainstem river contains 31 native and 25 non-native species. Abundance and species richness of native fish in both decades decreased longitudinally downstream, and abundance and richness of non-native fish increased downstream. In the mainstem Willamette in 2011-2013, 93% of the individual fish captured were native species. In monitoring of three major river tributaries in 2015-2017, 97% of the individual fish captured were native species. In the period of 2021-2023, abundance of non-native fish in the mainstem Willamette was significantly greater as compared to the previous decade, and the increase was greater in the downstream reaches of the river. Unlike the earlier mainstem monitoring, only 75% of the individual fish captured were native fish. Sixty percent of individual native fishes showed evidence of a decline in abundance or occupancy between decades, but absolute differences were relatively small for most species. Regional temperatures were exceptionally warm in 2015 and 2021. Decadal trends revealed that the greatest decline for native fishes of small cold streams and cool channels was in the upper mainstem, and the greatest decline for native backwater fishes occurred downriver. Non-native fishes, which are classified as warm-water tolerant, increased in abundance over the decade. This study demonstrates that a decade may be sufficient to detect changes in large river fish assemblages. Accelerated restoration efforts in rivers throughout the world are essential to protect and recover native fish assemblages. Restoration programs focused on correcting problems caused by past environmental degradation likely will be challenged by warming trends in many rivers. Success in restoring rivers and recovering native fish assemblages may be limited if we do not understand the processes that are changing and fail to anticipate the future river.