Fish stocking is used worldwide in conservation and management but its effects on food-web dynamics and ecosystem stability are poorly known. To better understand these effects and predict the outcomes of stocking, we used an empirically validated network model of a well-studied lake ecosystem. We simulate two stocking scenarios with two native fish species valuable for fishing. In the first scenario, we stock planktivorous fish (whitefish) larvae in the ecosystem. This leads to 1% increase in adult whitefish biomasses and decreases the biomasses of the top predator (perch). In the second scenario, we also stock perch larvae in the ecosystem. This decreases the planktivorous whitefish and the oldest top predator age class biomasses, and destabilizes the ecosystem. Our results demonstrate that the effects of stocking depend on the species’ position in the food web and thus cannot be assessed without considering interacting species. We further show that stocking can lead to undesired outcomes from both management and conservation perspectives. The gains of stocking can remain minor and have adverse effects on the entire ecosystem.