Ambitious to fulfill the European Water Framework Directive obligations, the European governments support projects to rehabilitate lakes with poor water quality. However, most lake restorations having relied on biomanipulation by fish thinning have failed to improve or even maintain water quality. Previous attempts removed all target fish species simultaneously, thus making it impossible to assess the specific impact of each feeding group on water chemistry. Lake Bromme was selected for extensive, time-selective fish biomanipulation to improve water clarity and promote submerged macrophytes and piscivorous fish stocks over a three-year monitoring period. Thinning of adult benthivorous bream (Abramis brama) and tench (Tinca tinca) was conducted throughout year one while thinning in years two and three targeted planktivorous roach (Rutilus rutilus), juvenile bream, and small perch (Perca fluviatilis). Yearly fish surveys assessed changes in fish population structure and biomass. Water quality parameters were monitored continually, and the cover of submerged macrophytes was surveyed annually via sonar. We found no improvement in water clarity or reductions of nutrients, organic particles, chlorophyll concentrations, or watercolor, despite a 6-fold thinning of total estimated fish biomass, from 112 to 19 kg ha−1. Over the period, the macrophyte cover increased from 0.8 to 13.5 %, but no recruitment of large piscivorous fish (perch and pike (Esox lucius) > 10 cm) was detected. We found higher correlations of particle concentration and water clarity to water temperature than to wind speed, which indicates sediment particle resuspension by the remaining fish community (mostly carp Cyprinus carpio) that forage on benthos in shallow lakes. Further system-ecological research in Lake Bromme should evaluate whether thinning the stock of carp and increasing plant cover may improve water quality and test which optical properties sustain high water turbidity and prevent shallow, eutrophic lakes like Lake Bromme from responding to intense fish thinning.