Freshwater macroinvertebrate communities may be changing over time with environmental changes and species introductions. This study aimed to explore macroinvertebrate communities in the Willamette River and its major tributaries, including long-term changes corresponding to the implementation of environmental flow regimes for the Sustainable Rivers Program beginning in 2011. We compare EPA-collected data of macroinvertebrates from 2006 to 2018 (Historical) to annual samples from 2022 to 2024 (Contemporary), noting changes in community structure and homogenization over time. We used non-metric multidimensional analysis (NMDS) to determine whether and how macroinvertebrate communities have changed, and variation partitioning to explain the extent to which ecological flows and associated physical variables may be contributing to this shift. We found a significant shift in macroinvertebrate communities, from historical communities that were more distinct by tributary to overlapping contemporary sites. Density and richness were higher in contemporary communities, but trait-based analyses suggest most ecological function has been maintained over time. The community composition changes appeared to correspond to years with lower flows and finer substrates. Community composition and traits may be important for ecological stability; the observed homogenization could be concerning, especially as communities respond to future disturbance.