Over the last two decades, the interest of microbial ecologists has been expanded from the study of individual lakes and streams to the structure of bacterial and protist communities across landscapes. A growing body of studies has repeatedly observed a drop in bacterial richness from upstream to downstream aquatic habitats, namely from inlet streams to lake pelagic environments; yet, the mechanism behind this diversity pattern remains unknown and the factors which regulate it largely uninvestigated. As part of my doctoral thesis, I study the microbial richness and composition in lakes and streams of a catchment area in Uppsala county, during three different seasons. I also investigate patterns of bacterial diversity in an aquatic network in Jämtland, comprised of three lake chains. Last but not least, I aim to explore whether migrating bacteria from upstream habitats have the potential to successfully establish in downstream lakes through a series of in vitro transplant experiments. These questions are key to further investigate the mechanism behind the changes of microbial diversity along aquatic networks.