Major Baltic inflow (MBI) events carry highly saline water from the North Sea to the central Baltic Sea and thereby affect both the environmental conditions and the biota in the Baltic’s deeper layers. While bacterioplankton communities in the Baltic Sea are strongly structured by its salinity, how MBIs impact the composition and distribution of those communities is unknown. However, insights into this relationship were afforded by an exceptional MBI in 2014 that brought saline and oxygenated water into the basins of the central Baltic Sea. Following this event, we analyzed bacterioplankton community composition in the inflowing water and in the uplifted former bottom water at stations in the Western and central Baltic Sea that were reached by the MBI. Bacterial diversity data were compared with data on the respective communities obtained during a previous non-inflow situation involving the same locations. In contrast to the broad taxonomic changes in bacterial community composition that are generally associated with changes in salinity, significant changes following the 2014 MBI were mainly at the genus level. The relative similarity of the bacterial communities in the inflowing and uplifted waters as well as the results from an inflow-simulating numerical model indicated that the inflowing water did not originate directly from the North Sea but mostly from adjacent areas in the Baltic Sea. These findings further suggested that the inflow event led to a series of shifts in Baltic Sea water mass among the Baltic Sea basins and a gradual mixing of the water bodies. Dramatic changes in bacterial community composition between inflowing and uplifted waters did become visible when the bottom-water inflow reached the anoxic, sulfidic deep basins, resulting in an uplifting of the former anoxic bacterial community, dominated by the Epsilonproteobacterium Sulfurimonas spp., to water depths within the oxygenated layer. Our study of the impact of MBIs on bacterioplankton communities therefore highlights two relevant underlying mechanisms that impact the distribution and possibly also the activities of planktonic bacteria in the Baltic Sea: the successive dilution of inflowing North Sea with ambient waters and the uplifting of former bottom-water communities to higher water strata.