In working towards understanding ecosystems that are often dominated by microorganisms, aquatic ecologists have historically relied on measuring bulk, community-level properties and synecological processes. However, developing a mechanistic and predictive explanation for the factors structuring aquatic ecosystems will require understanding the roles that individual microorganisms play in these higher-order phenomena. The application of molecular biological techniques to examine nucleic acids extracted in bulk from microbial communities can provide information about the taxonomic structure of microbial communities and the physiological ecology of particular types of organisms at various levels of specificity. Yet, even if accomplished at the ‘species' level, these data still represent bulk parameters because they can reveal only an average value for the organisms and community of interest. A more detailed view may be gained by investigations performed at a single-cell level. Flow cytometry allows the measurement of one cell at a time, at a rate of thousands of cells per second. When combined with fluorescent stains, including nucleic acid and antibody-based molecular probes, flow cytometry permits rapid analysis of cell-specific information for particular types of microbes within complex microbial assemblages. Thus, the autecology of microbial populations and structure of microbial communities can be examined from the vantage point of the individual cells comprising them. By bringing the level of analysis closer to the relevant scale of the organisms being investigated, the combination of molecular tools and flow cytometry will bring powerful new insights into the autecology of aquatic microorganisms.