Systematic conservation planning has become a standard approach globally, but prioritization of conservation efforts hardly considers species traits in decision-making. This can be important for species persistence and thus adequacy of the conservation plan. Here, we developed and validated a novel approach of incorporating trophic information into a systematic conservation planning framework. We demonstrate the benefits of this approach by using fish data from Europe´s second largest river, the Danube. Our results show that adding trophic information leads to a different spatial configuration of priority areas at no additional cost. This can enhance identification of priority refugia for species in the lower position of the trophic web while simultaneously identifying areas that represent a more diverse species pool. Our methodological approach to incorporating species traits into systematic conservation planning is generally applicable, irrespective of realm, geographical area and species composition and can potentially lead to more adequate conservation plans.