The main response to arsenic contamination of shallow tubewells in Bangladesh is the provision of alternative water supplies. To support decision-making in relation to alternative water supply selection, the Arsenic Policy Support Unit commissioned the development of a tool for estimating disease burdens for specific options using disability-adjusted life years as the metric. This paper describes the assumptions in dose-responses, relationships between microbial indicators and pathogens, water consumed and population characteristics used, and presents a case study of how the tool was applied. Water quality data and dose-response models were used to predict disease burdens due to microbial pathogens and arsenic. Disease burden estimates predicted by the tool were based on evidence in the published literature. There were uncertainties in key assumptions of water consumed and the ratio of microbial indicators and pathogens, which led to broad confidence intervals and the need to consider the results in a wider context and further research needs. Deep tubewells and rainwater harvesting had the lowest disease burden estimates, while pond sand filters and dug wells had much higher predicted disease burden due to frequent microbial contamination. The need for rigorous water supply protection through water safety plans was highlighted. At present, the risk assessment is useful for informing judgement by experienced water and health professionals and identifying key research questions. Improved arsenic dose-response models and a better understanding of the relationship between microbial indicators and pathogens in tropical settings are required.