This is the first reported study of a riverbank filtration (RBF) scheme to be assessed following the Australian Guidelines for Managed Aquifer Recharge. A comprehensive staged approach to assess the risks from 12 hazards to human health and the environment has been undertaken. Highest risks from untreated ground and Ganga River water were identified with pathogens, turbidity, iron, manganese, total dissolved solids and total hardness. Recovered water meets the guideline values for inorganic chemicals and salinity but exceeds limits for thermotolerant coliforms frequently. A quantitative microbial risk assessment undertaken on the water recovered from the aquifer indicated that the residual risks of 0.00165 disability-adjusted life years (DALYs) posed by the reference bacteria Escherichia coli O157:H7 were below the national diarrhoeal incidence of 0.027 DALYs and meet the health target in this study of 0.005 DALYs per person per year, which corresponds to the World Health Organization (WHO) regional diarrhoeal incidence in South-East Asia. Monsoon season was a major contributor to the calculated burden of disease and final DALYs were strongly dependent on RBF and disinfection pathogen removal capabilities. Finally, a water safety plan was developed with potential risk management procedures to minimize residual risks related to pathogens.