Fish migration barriers impose a strong disturbance on freshwater food webs by removing top predators in the system. These shifts have profound impacts on the structure of the food web, releasing pressure on lower trophic levels and shifting the structure of various benthic communities. In Northern California, USA, Big Chico Creek is one of the last remaining undammed waterways of the region, featuring a natural flow regime, but with existing fish barriers due to past geologic and human activity. However, a future restoration project is aimed at removing these fish barriers and restoring connectivity for anadromous salmonid migrations. Here, we analyzed the existing benthic macroinvertebrate (BMI) communities for changes in structure moving through the longitudinal gradient of the stream, incorporating fish barriers and other human-associated disturbances. These data will serve as a baseline for future studies documenting the impact of barrier removal.