New technologies have enabled researchers to peer into the ‘black box’ of freshwater bacterial community structure. Inland waters are home to an assemblage of bacteria that is distinct from terrestrial and marine communities, and the various freshwater bacterial groups have distinctive lifestyles and habitat distributions. These bacteria form communities that are highly diverse but tend to be dominated by a few species at any given time. The identity of the dominants can change rapidly in relation to changing environmental conditions and biological interactions. Some of the important environmental factors that have been shown to structure lake bacterial communities include temperature, oxygen concentration, water clarity, pH, humic acid content, salinity, nutrient concentration, water column mixing, water residence time, and toxic metals. The influence of these factors defines changing patterns in bacterial community composition in space and time. Bacterial communities are also structured by biological interactions such as competition, predation by nanoflagellate grazers and zooplankton, viral lysis, and linkages to algae. Under the influence of these structuring forces, bacterial dynamics suggest communities in varying states of recovery from ecological disturbances that may serve to maintain the high diversity of freshwater bacterial communities.