Within the benthic realm life carpets the sedimentary surface of all aquatic ecosystems including the oceans, lakes, rivers and streams. Microorganisms of all types, bacteria, archaea and eukaryotes, inhabit these environments and through their metabolic activities contribute to the biogeochemical cycles that sustain life on earth. In this chapter we address the question "Why live on or in sediments, or in some cases, attached to rocks or other hard surfaces?" and then explore major questions in the ecology of benthic microbial life in freshwater and shallow marine systems and current methodological approaches used in addressing these questions. Our first focus is on the abiotic and biotic factors that strongly influence the distribution and abundance of benthic microorganisms. Elemental cycles and the possibility of bacterial biogeography within the benthic realm are also addresses. Obtaining high quality samples and methods for determining microbial activity, biomass and community structure are discussed with classical/direct observation, biochemical and molecular approaches highlighted. Characterization of dissolved organic matter, methods for foodweb analysis and identification of the active component of microbial communities are specifically addressed. We conclude with a brief examination of several current questions within the general field of benthic microbial ecology.