The life histories of many organisms are directly tied to floodplain inundation for access to spawning grounds, nurseries, and feeding, but many floodplain ecosystems have been altered by anthropogenic activities and are disconnected from associated rivers. The Atchafalaya River Basin (ARB) floodplain, Louisiana, is relatively intact, whereas the upper Barataria Estuary (UBE) has been separated from the Mississippi River by anthropogenic modifications and lacks an annual flood pulse. The lack of connection can alter trophic webs that include fish species such as bowfin (Amia calva). Therefore, bowfin diets in these two floodplain ecosystems were examined to determine if the difference in floodplain connectivity was associated to bowfin diets. Bowfin were collected by boat electrofishing in the ARB (n = 89) and UBE (n =143) from March 2017 to August 2017. Mean percent empty stomachs was similar between basins, with 26% empty in the ARB and 30% in the UBE. Bowfin diets in both basins were composed primarily of crayfish and fish, but crayfish composed a higher proportion of bowfin diets in the ARB compared to the UBE. Overall, diets of bowfin were very similar between basins. However, fish consumed by bowfin in the ARB were primarily bowfin and sunfish (Lepomis spp.) whereas bay anchovy (Anchoa mitchilli) and unidentified fish were the preference of bowfin in the UBE. Bowfin in the UBE also had a more diverse diet which included insects, amphibians, and reptiles. This study provides a baseline to evaluate effects of floodplain inundation on trophic dynamics as coastal restoration activities progress and may be used as a tool to assist in evaluation of restoration measures.