Most stream fish communities have changed over time in response to common anthropogenic disturbances. Impoundments are a widespread anthropogenic stressor that can negatively impact stream fishes as they alter flow regimes, block movements, and act as fountainheads for the introduction and spread of invasive species. Recent studies, however, have reported the occurrence and reproduction of native fishes in impoundments, suggesting they might benefit some native fishes. Our primary objective was to evaluate whether impoundment construction has led to changes in fish community structure in prairie streams. To accomplish this, we compared fish occupancy in small impoundments (,5 ha) to temporal trends in stream occupancy among species to test whether species' increases in stream occupancy were related to their occupancy in impoundments. We examined stream fish communities in the Upper Cottonwood River basin, Kansas, from 1948–2018, and sampled small impoundments in 2016 and 2017. A third (32%) of fish communities in impoundments were similar to stream assemblages, whereas most impoundments (68%) were dominated by sport or bait fishes. In streams, six species showed increases in occupancy and four species showed decreases since small impoundment construction. Of the species that exhibited increased stream occupancy, five showed a positive, logistical relationship between a species' impoundment occupancy and its increase in stream occupancy. Species declining in stream occupancy experienced continued linear declines and may still be declining. Our research suggests stream fish communities have changed since impoundment construction, and are associated with locally-invasive, native species reaching a new stable state in streams accompanied by declines in other native stream fish species.