Microorganisms are key players in terrestrial and aquatic ecosystems, controlling allmajor biogeochemical fluxes of elements. Although the study of microbial ecology goesback several decades, our ability to understand or predict the taxonomic and functionalresponses of microbial communities to changes in environmental conditions remainslimited. One of the reasons may be that microbial communities may contain species thatare not adapted to the local environment and do not contribute to community functioning, given that microorganisms can be dispersed long distances and can persist inactiveout of their suitable habitats for long periods. The advent of sequencing technologies,which enabled an improved access to microbial diversity and expanded the scale of studies, revealed that microbes often form part of larger metacommunities in which local assemblages are linked by the dispersal of species. However, disciplines such as microbiallimnology and oceanography (the study of freshwater and marine microorganisms, respectively) often operate in isolation, providing a fragmented view of a naturally connected microbial world. This review seeks to summarize what we have learnt over the past fewyears regarding the effect of microbial dispersal and connectivity on the structuring andfunctioning of aquatic microbial communities, with particular emphasis on bacterioplankton assemblages. These investigations have highlighted that terrestrial, freshwaterand marine microbiomes are intimately linked by the transport of taxa through flowingwater, the air, or processes such as marine particle sinking, and hence that understandingthe drivers and ecological consequences of microbial ecology and biogeography requiresgoing beyond ecosystem boundaries. Sharing knowledge and expertise between traditionally independent disciplines will be essential to advance towards a more holistic view ofmicrobial ecology that considers species linkages between different ecosystems.