As drivers of biogeochemical cycles and nutrient recycling, such as carbon turnover, the microbial community is essential in sustaining functioning ecosystems. Together with the metazoan community, the microbial community constitute the majority of all life in the benthos. Environmental change in biotic and abiotic factors may influence the dynamics of these communities, for example through a sorting or driving effect on the community structure through assembly processes. Environmental change, e.g. change in dissolved oxygen concentration, salinity and temperature, can directly or indirectly affect community composition. How, in what way, and to what extent, benthic bacterial and meiofaunal community composition in the eutrophied, brackish benthic environments, in the Baltic Sea sub-basin the Baltic Proper, respond to environmental change is understudied, both at local and seascape scale. This thesis aimed to study and understand the effects of environmental variation on the diversity and biogeographic patterns of Baltic Sea sediment bacterial and meiofaunal communities. A further aim was to understand the links between the different community levels by studying the interaction between meiofaunal- and macrofaunal communities in relation to environmental variation. Community diversity was analysed along a latitudinal transect of national environmental monitoring stations in the Baltic Proper using a framework of metapopulation and metacommunity theory. The analyses were based on environmental genomics, with high-throughput sequencing, bioinformatics and statistics. The total community genome was analysed using phylogenetic marker gene fragments as a proxy for taxonomic diversity, to investigate diversity, community structure and dynamics. Salinity and oxygen were found to be the main abiotic environmental drivers of benthic community composition and alpha- and beta-diversity patterns. Furthermore, macrofauna-meiofauna interactions were significantly more complex in higher salinity environments. Results also showed that both enhanced environmental gradients and dispersal following a major inflow of saline and oxygenated water from the Atlantic Ocean, influenced the composition of sediment bacterial communities at the seascape scale of the Baltic Sea, as shown by a reduced beta-diversity and increased alpha-diversity, and the development of a significant distance-decay of community similarity. This study also identified strong metapopulation dynamics of the benthic sediment bacterial communities with many satellite and a few core taxa. The outcomes from this study contribute to the understanding of how environmental variation and environmental change relate to changes in Baltic Sea benthic community diversity and composition, and important factors and processes governing community dynamics.