[Truncated abstract] Managed Aquifer Recharge (MAR) is a technique that can be used to capture and store water in aquifers for later reuse. This method recycles water that would normally be lost or discarded to the environment. MAR has been observed to have the potential for improving the quality of recharged water through a combination of physical, chemical and biological processes. The aim of this study was to investigate the changes in groundwater microbial population structure during MAR and the major influences that drive these population changes. Biogeochemical MAR studies have the potential to assist in the improved prediction of the removal of contaminants such as nutrients, pathogens and trace organics from the recharged water. Biological clogging during recharge also has the potential to overwhelm an aquifers ability to process wastewater thus reducing the hydraulic conductivity of the aquifer. Therefore further research into the spatial and temporal biogeochemical processes that occur during MAR is required. The geochemical and microbial population dynamics of two contrasting MAR techniques were investigated at two different geographical locations (Perth, Western Australia and Adelaide, South Australia). These MAR sites contained aquifers of dissimilar properties that were recharged with wastewater that contrasted in water quality. The Perth MAR site received secondary treated effluent which continuously infiltrated the unsaturated zone into an unconfined aquifer aided by infiltration galleries. Reclaimed water was extracted from a well at distance from the infiltration gallery. ... Notably the background and recovered water was most dissimilar in microbial and chemical population structure to that described for the infiltration gallery and injection well. Microbial and chemical evidence suggested that the background and extraction well groundwater were unaffected by plume migration. These results suggested that extraction well groundwater was similar in quality to that of ambient groundwater. Significant geochemical and microbial changes of secondary treated effluent during infiltration and lateral movement through aquifer were implicated in addition to the forced hydraulic gradient created from extracting fives time the volume of infiltrating wastewater. This study demonstrated that microbial populations and the geochemical processes associated with MAR can be studied and compared. Multivariate statistical methodology greatly simplified a vast array of dynamic biogeochemical information that could be dissected for meaningful interpretation over distance and time. The study evaluated the major biogeochemical influences which resulted in microbial and geochemical changes where it was noted that microbial populations were more dynamic than geochemical variation over time. Additionally biogeochemical comparative analysis indicated that microbial populations could change in population structure before a shift in aquifer geochemistry was detected. It is anticipated that the results from this study will benefit further research into the biogeochemical processes involved in water quality changes (e.g. nutrient removal, pathogen decay and biodegradation of trace organics) as well as controlling biological clogging of MAR schemes.