Dam construction affects freshwater ecosystems worldwide. While there is much focus on large impoundments, farm ponds are overlooked despite their near-ubiquity across human-altered landscapes. Within the Great Plains of North America, there are millions of farm ponds, yet little is known about the fish communities and factors structuring them. We propose a conceptual model where fish, amphibian, and crayfish abundances differ along a pond size and water permanency gradient and are further influenced by interactions among species. In the summer of 2021, we sampled 100 farm ponds across central Kansas, primarily on private land. Pond size and permanency explained community structure with smaller and less permanent ponds being dominated by amphibians and crayfish while larger ponds were dominated by stocked sportfish. Distribution modeling revealed a negative correlation between stocked fish and other community components indicating potential interactions. If we are to conserve headwater stream species, especially those that are threatened or endangered, strategies that integrate farm ponds seem necessary given their prevalence on the landscape.