Fish stocking is used worldwide for conservation and management purposes but its effects on food-web dynamics and ecosystem stability are poorly known. To better understand these effects, an empirically validated network model was used to study a well-studied lake ecosystem. Two stocking scenarios with two native fish species valuable for fishing were simulated. In the first scenario, whitefish larvae were stocked in the ecosystem. This led to a minor increase in adult whitefish biomasses and decreased perch biomasses. In the second scenario, also perch larvae were stocked in the ecosystem. This led to a decrease in whitefish biomasses and in the biomass of the old perch, and destabilized the ecosystem. The effects of stocking depend on the species’ position in the food web and thus cannot be assessed without considering interacting species. Our results show that fish stocking can change dynamics of an aquatic food web and lead to undesired outcomes from both management and conservation perspective.