The size structure of populations is crucial for predator–prey dynamics and ecosystem function. Anthropogenic pressures such as habitat alteration may affect the demography of many species. We investigated the size structure of European perch (Perca fluviatilis) populations in lakes before and after dam removal by using the planned removals of multiple dams in the outlets of boreal lakes in central Sweden as a natural experiment. In five lakes from which we had obtained data both before and after dam removal, removal resulted in a reduced abundance of small perch and an increase in body size of large, piscivorous perch, but there was no major effect on perch biomass. In a second comparison of 22 lakes where we only had access to data from either before or after removal, the effects were not as evident. We suggest that a plausible mechanism explaining a potential effect on perch demography was alterations in the predator–prey dynamics caused by changes in refuge habitat area for small fish. Specifically, dam removal caused a reduction of aquatic plant coverage. Large piscivorous fish are known to play a crucial regulatory role in controlling lake ecosystem function. Thus, we suggest that lake outlet dam removal may induce processes leading to positive effects on fish populations and ecosystem state. Moreover, our study emphasises the importance of before versus after studies to evaluate restoration measures.