The primary aim of this data product is to characterize change in water chemistry, sediment-water interactions, and biological communities in shallow, eutrophic lakes undergoing a fishery biomanipulation. We studied eight glacial lakes located in northwest Iowa, USA, from 2018 to 2020 during the summer season (May to September). A subset of these lakes (n = 4; Center, Five Island, North Twin, and Silver Lakes) were part of a fishery biomanipulation in which the Iowa Department of Natural Resources (IDNR) incentivized commercial harvest of common carp (Cyprinus carpio) and bigmouth buffalo (Ictiobus cyprinellus). Harvests occurred in Center and Five Island Lakes during 2018-2019 and in North Twin and Silver Lakes during 2019-2020. Between 73 and 373 kg fish biomass per ha were removed each year. The other study lakes (n = 4; Blue, South Twin, Storm, and Swan Lakes) remained unmanipulated during the study period. Over the course of the biomanipulation, we quantified a suite of physical, chemical, and biological parameters across the study lakes. High frequency aquatic sensors were used to measure water column thermal structure, dissolved oxygen concentrations, and algal pigments. Manual water chemistry sampling further quantified suspended solids, total phosphorus and nitrogen, soluble reactive phosphorus, nitrate, and water clarity. We measured flux rates of phosphorus between bottom sediments and the overlying water using ex situ sediment core incubations under both oxic and anoxic conditions. We further quantified sediment phosphorus sorption capacity using equilibrium phosphorus concentration assays. Tiered sediment traps were used to measure sedimentation rates as well as sediment resuspension in bottom waters. We also measured change in zooplankton, macroinvertebrate, and macrophyte community composition and abundance. These data will be used to better understand the mechanisms of internal phosphorus loading in shallow lakes and the ecosystem effects of fisheries biomanipulations. This knowledge will inform local management and lake restoration activities as well as a broader understanding of shallow lakes and organism-ecosystem interactions.