Technical Abstract: Primary samples of groundwater and core are collected and analyzed to characterize the microbiology of aquifers and to estimate or predict biogeochemical transformations. Alternative sampling devices have been developed that are incubated for some length of time in the aquifer to accrue biomass for analysis. The applicability of each of these types of samples to accurately reflect aquifer microbial populations and processes is often undetermined. Site-specific conditions may influence the suitability of different sampling approaches. This paper explores the understanding of aquifer microbiology in the context of sampling approaches used at different sites over the last three decades, and suggests areas requiring further study.