Abstract Bioturbation (sediment disturbance by animal actions) effects on nutrient cycling and nutrient levels in surface waters are difficult to quantify, in part because the diversity and magnitude of species‐specific influences are poorly understood. These influences may have consequences for the management of the trophic state of freshwater ecosystems. Fish cause bioturbation in freshwater and marine ecosystems by digging in benthic sediments, manipulating periphyton mats while searching for prey and scraping hard substrates while feeding. We used experimental enclosures (2.25 m2) to quantify bioturbation‐mediated phosphorus (P) and nitrogen (N) regeneration from sediment by three species of fish that differ in interactions with the benthos (largemouth bass, Micropterus salmoides; tilapia, Oreochromis spp.; and sailfin catfish, Pterogoplichthys spp.) in shallow eutrophic wetlands in Southern Florida. Tilapia are omnivores that include detritus in their diet (winnowing or ingesting sediments) and dig nests in soft sediments year round, sailfin catfish actively burrow into substrate and consume detritus (digging and ingesting sediments), and largemouth bass are piscivores that do not routinely interact with the benthos when feeding but may dig nests in soft sediment in spawning season (January–April). We quantified the amount of suspended flocculent organic matter and changes in water column nutrients (total phosphorus [TP] and total nitrogen [TN]) in 2‐week trials for each species and estimated the portion of nutrient increases relative to fishless controls that could be attributed to bioturbation‐mediated internal nutrient loading through suspension of organic matter (as opposed to excretion or other sources of nutrient loading). Water column nutrient concentrations increased with increasing biomass for all species, but the bioturbation contribution differed by species. Largemouth bass increased water column nutrient concentrations (TP: 86% and TN: 5% relative to controls) but did not influence water column suspended particulate matter through bioturbation of sediment. Tilapia increased water column nutrients a modest amount (TP: 8%; TN: 15%), of which a small portion was attributed to bioturbation (c. 18% of TP). Sailfin catfish raised water column nutrients substantially (TP: 105%; TN: 46%) and up to 100% of the increased TP was attributed to bioturbation. Sailfin catfish also suppressed algal growth and TP accumulation on the sides of the enclosures and reduced nutrient concentrations of the flocculent sediments. Our results were consistent with our hypothesis that behaviour and foraging traits affect bioturbation contributions to nutrient loading. The results also demonstrated that species with similar net effects like largemouth bass and sailfin catfish, added nutrients via different mechanisms (i.e. excretion vs. bioturbation). Considering the feeding strategies and interactions with the substrate of common fish species may assist managers in meeting nutrient reduction goals for eutrophic wetlands and managed freshwater systems.