As the important part of earth's critical zone, groundwater system provides special habitat environment and complex conditions for microorganisms, which further evolves complicated biogeochemical processes. In the last decades, with the developing and inter-crossing of new technologies and multi-discipline, important progresses have been obtained in the fields of microbial functional communities and biogeochemical cycle in groundwater. This review mainly describes the ecological niche of functional microbial communities, introduces the new findings in microbially-mediated geochemical cycling, microbial remediation and numerical simulation of the biogeochemical processes in groundwater system, including the discovery of new species, the coupling of various element cycles, and the latest technology of in-situ remediation of contaminated groundwater. This work also prospects the related future research direction including the microbial "dark matters" and "dark processes", bioremediation, medical geology, and multidisciplinary integration in groundwater system.