This chapter focuses on the various methods to study the bacterial ecology of freshwater environments. This chapter discusses the bacteria in lakes that are divided into the assessment of numbers and activity with respect to synecological or autecological studies. It is not intended to provide detailed descriptions of the techniques, as virtually all the methods will have to be adapted for the habitat under study. This is particularly true of sediment systems for which reagents may have to be modified, because of the changes in the composition of the sediment. As the knowledge of the activity and interaction of aquatic bacterial populations increases the limitations of various methods become apparent. Methodology will and must continue to develop, as information or technology becomes available. Such developments will ultimately allow accurate assessment of the role of bacteria in freshwater environments.