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Martin A. Simonson, Michael J. Weber, Grace M. Wilkinson and Andrew R. Annear. 2023. Annual changes in water quality and sportfish community structure following commercial harvest of common carp and bigmouth buffalo. Lake Reserv Manage. 39:174–189. Commercial harvest of common carp ( Cyprinus carpio ; hereafter carp) and bigmouth buffalo ( Ictiobus cyprinellus ; hereafter buffalo) populations had little detectable effect on shallow lake ecosystems. We tested whether carp and buffalo biomass removal affects limnological variables and fish community metrics across 6 shallow, natural lakes of northwestern Iowa using mixed effects models. Annual commercial harvest of carp ranged from 0 to 71 kg/ha; annual harvest of buffalo ranged from 0 to 356 kg/ha. Biomanipulation (i.e., commercial harvest) of carp was associated with decreases in soluble phosphorus and nitrogen concentrations, but not total phosphorus or nitrogen. Buffalo harvest was unrelated to annual changes in nutrient concentrations but was associated with reductions in chlorophyll  a  and phycocyanin concentrations. Secchi disk transparency and total suspended solids were unrelated to carp and buffalo harvest. Carp harvest was associated with reduced biomass of large cladocerans but no other zooplankton biomass densities; buffalo harvest was unrelated to zooplankton biomass. Species richness and rake density of aquatic macrophytes were unrelated to carp and buffalo harvest. Carp and buffalo harvest was unrelated to changes in most indices of sportfish abundance, condition, and size distribution. Our results suggest harvest of carp and buffalo &lt;71 kg/ha has little effect on abiotic and biotic ecosystem components on short time scales and highlights the challenges associated with shallow lake restoration.