The invasive American bullfrog (Lithobates catesbeianus) and a variety of non‐native sport fish commonly co‐occur in lowland lentic habitats of the western United States. Both invasive taxa are implicated in declines of native amphibians in this region, but few long‐term studies of communities exist. Further, field studies of invasive–native interactions are complicated by confounding habitat modifications and observation errors. We surveyed amphibians and measured habitat characteristics for 12 yr across 38 wetland sites within the Willamette Valley, Oregon, USA. We assessed the influence of invasive species, habitat, and their interactions on the distributions of five native amphibian species using a multispecies dynamic occupancy model that accounted for false‐negative and false‐positive detections. In general, habitat characteristics—such as within‐pond vegetation cover, surrounding forest, and drought severity—were important for local persistence of native species when bullfrogs co‐occurred. We also found evidence of a cumulative negative effect of bullfrogs and non‐native fish (families Centrarchidae and Ictaluridae) on northern red‐legged frog (Rana aurora) local persistence that was mediated by the dominance of invasive reed canarygrass (Phalaris arundinacea). Non‐native fish and bullfrogs had variable effects on native amphibian species, but neither invasive taxon appears to be causing declines in occupied sites within our study area. Moreover, species relationships with habitat differed when invaders were present, indicating that certain habitats may increase persistence of native amphibians in the invaded landscape.