Alien species contribute to global change in all marine ecosystems. Environmental variability can affect species distribution and population sizes, and is therefore expected to influence alien species. In this study, we have investigated temporal variability of 11 alien species representing different trophic levels and ecological functions in two gulfs of the brackish Baltic Sea in relation to environmental change. Independent of the invasion time, organism group or the life-history stage, abundance and/or biomass of the investigated alien species was either stable or displayed abrupt increases over time. Timing in population shifts was species-specific and exhibited no generic patterns, indicating that the observed large shifts in environmental parameters have no uniform consequences to the alien biota. In general, the inter-annual dynamics of alien and native species was not largely different, though native species tended to exhibit more diverse variability patterns compared to the alien species. There were no key environmental factors that affected most of the alien species, instead, the effects varied among the studied gulfs and species. Non-indigenous species have caused prominent structural changes in invaded communities as a result of exponential increase in the most recent invasions, as well as increased densities of the already established alien species.