The conservation and sustainable use of freshwater resources is of global importance. Microorganisms are not only the most abundant organisms in natural freshwater systems, but are also key players in ecological processes controlling water quality. Detailed knowledge of the diversity and function of microorganisms dwelling in freshwater habitats is an essential prerequisite for the sustainable management of freshwater resources. Freshwater systems are inhabited by microbial communities that are indigenous to this habitat type and usually do not occur in marine systems, saline inland waters and terrestrial habitats. Despite recent advances in the characterization of the diversity of freshwater microorganisms, knowledge essential for a holistic understanding of their ecological roles is still lacking.