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Background In recent decades, many attempts have been made to restore eutrophic lakes through biomanipulation. Reducing the populations of planktivorous and benthivorous fish (either directly or through stocking of piscivorous fish) may induce ecosystem changes that increase water transparency and decrease the risk of algal blooms and fish kills, at least in the short term. However, the generality of biomanipulation effects on water quality across lake types and geographical regions is not known. Therefore, we have undertaken a systematic review of such effects in eutrophic lakes in temperate regions throughout the world. Methods Searches for literature were made using online publication databases, search engines, specialist websites and bibliographies of literature reviews. Search terms were developed in English, Danish, Dutch and Swedish. Identified articles were screened for relevance using inclusion criteria set out in an a priori protocol. To reduce the risk of bias, we then critically appraised the combined evidence found on each biomanipulation. Data were extracted on outcomes such as Secchi depth and chlorophyll a concentration before, during and/or after manipulation, and on effect modifiers such as lake properties and amounts of fish removed or stocked. Results Our searches identified more than 14,500 articles. After screening for relevance, 233 of them remained. After exclusions based on critical appraisal, our evidence base included useful data on 128 biomanipulations in 123 lakes. Of these interventions, 85% had been made in Europe and 15% in North America. Meta-analysis showed that removal of planktivores and benthivores (with or without piscivore stocking) leads to increased Secchi depth and decreased chlorophyll a concentration during intervention and the first three years afterwards. Piscivore stocking alone has no significant effect. The response of chlorophyll a levels to biomanipulation is stronger in lakes where fish removal is intense, and in lakes which are small and/or have high pre-manipulation concentrations of total phosphorus. Conclusions Our review improves on previous reviews of biomanipulation in that we identified a large number of case studies from many parts of the world and used a consistent, repeatable process to screen them for relevance and susceptibility to bias. Our results indicate that removal of planktivorous and benthivorous fish is a useful means of improving water quality in eutrophic lakes. Biomanipulation tends to be particularly successful in relatively small lakes with short retention times and high phosphorus levels. More thorough fish removal increases the efficacy of biomanipulation. Nonetheless successes and failures have occurred across a wide range of conditions.