The number of non-indigenous aquatic species (NIS) has rapidly increased globally. The majority of published evidence on the effects of NIS on local communities is from single species studies in which the interactive effects of NIS are not considered. Here we present experimental evidence of separate and interactive effects of two widespread non-indigenous benthic predators, the round goby (Neogobius melanostomus) and the North American mud crab (Rhithropanopeus harrisii) on benthic invertebrate communities in a shallow coastal ecosystem of the Gulf of Riga, the Baltic Sea. The two species have recently colonized multiple sub-basins of the Baltic Sea and due to their rapid range expansion, increasing densities and local functional novelty, they are expected to have strong separate or interactive effects on native communities. Our laboratory experiment demonstrated that round goby and mud crab exerted a significant predation pressure on different benthic invertebrate species and the effects of the studied predators were largely independent. Predation was stronger at higher temperature compared with low temperature treatment. Among the studied invertebrate species gammarid amphipods were consumed the most. Interestingly, round goby did not prey on the mud crabs despite a large size difference of the studied predators.