AbstractAnthropogenic disturbances, including non-indigenous species (NIS) and climate change, have considerably affected ecosystems and socio-economies globally. Despite the widely acknowledged individual roles of NIS and global warming in biodiversity change, predicting the connection between the two still remains a fundamental challenge and requires urgent attention due to a timely importance for proper conservation management. To improve our understanding of the interaction between climate change and NIS on biological communities, we conducted laboratory experiments to test the temperature and pCO₂ tolerance of four gammarid species: two native Baltic Sea species (Gammarus locusta and G. salinus), one Ponto‐Caspian NIS (Pontogammarus maeoticus) and one North American NIS (Gammarus tigrinus). Our results demonstrated that an increase in pCO₂ level was not a significant driver of mortality, neither by itself nor in combination with increased temperature, for any of the tested species. However, temperature was significant, and differentially affected the tested species. The most sensitive was the native G. locusta which experienced 100% mortality at 24 °C. The second native species, G. salinus, performed better than G. locusta, but was still significantly more sensitive to temperature increase than either of the NIS. In contrast, NIS performed better than native species with warming, whereby particularly the Ponto-Caspian P. maeoticus did not demonstrate any difference in its performance between the temperature treatments. With the predicted environmental changes in the Baltic Sea, we may expect shifts in distributions of native taxa towards colder areas, while their niches might be filled by NIS, particularly those from the Ponto-Caspian region. Although, northern colder areas may be constrained by lower salinity. Additional studies are needed to confirm our findings across other NIS, habitats and regions to make more general inferences.