Water scarcity combined with high incidences of diarrhoeal disease amongst many rural communities, suggests that the provision of 'safe' water supplies remains a challenge. Subsequent reliance on multi-source water supplies means that microbial transmission pathways may be numerous and complex.This study aimed to identify and elucidate water supply issues and potential microbial transmission pathways at the household level in rural communities in semi-arid Brazil.Community and sanitary surveys were applied to 99 households from 10 communities located in four municipalities of Paraiba State, Brazil. Moreover, physicochemical and microbial parameters were investigated throughout the water supply chain.High levels of faecal indicator organisms (FIO) were detected in water from Water Storage Reservoirs (WSR) and from in-house Drinking Water Storage Containers (DWSC). A decrease in microbial water quality was observed between water stored within WSR's and DWSC's, suggesting potential cross-contamination at the household level. Several common practices were observed among rural residents, such as the use of collection buckets left unprotected outside on the ground, that may have also contributed to the observed decrease. Schematic diagrams illustrating the complex water supply chains and potential microbial transmission pathways were developed to facilitate identification of effective intervention strategies.Decreases in water supply quality were found to be predominantly caused by cross-contamination within the domestic environment due to several factors, including, a lack of awareness and knowledge of 'safe' collection, handling and storage of water, as well as inadequate sanitation services and/or unhygienic practices. In order to improve public health in such communities, more effort should be directed towards education and training of all stakeholders involved in the water supply chain. This would, certainly, support the successful implementation of further WASH interventions, consequently increasing the likelihood of achieving reduction of excreta-borne diseases.