Fishes have spread into previously fishless wetlands, likely affecting other species. In the Prairie Pothole Region of North America, the invasion of fish into wetlands is facilitated by interactions of altered land use, climate, and hydrology. We aimed to understand the effects of fishes on amphipods, which are macroinvertebrates that vertebrates rely on as forage. We hypothesized the presence and abundance of fish, particularly benthivores, would have detrimental effects on amphipod abundance. Our study design targeted a large gradient of amphipod abundances among wetlands, including very high abundances of two amphipod species: Gammarus lacustris and Hyalella azteca. We found that fishless basins had twice as many amphipods as those with fish, on average. Gammarus lacustris were not detected in the presence of Black Bullhead Ameiurus melas. The abundance of both amphipod species had negative associations with the most common fishes, Fathead Minnow Pimephales promelas and Brook Stickleback Culaea inconstans. A multivariate community analysis showed the benthivore-fish functional feeding guild was negatively associated with the amphipod community, as hypothesized. However, our study design captured several wetlands with anomalies of high abundances of both fish and amphipods, obscuring their relationships. Our results aid resource managers by confirming several fish guilds and species are associated with lower abundances of amphipods. These findings can inform resource managers who make decisions about managing for fish and wildlife; for example, they may choose to manage existing fish populations or protect existing wetlands with high amphipod densities from new fish invasions.