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IntroductionDespite clear linkages between provision of clean water and improvements in child health, limited information exists about the health impacts of large water infrastructure improvements in low-income settings. Billions of dollars are spent annually to improve urban water supply, and rigorous evaluation of these improvements, especially targeting informal settlements, is critical to guide policy and investment strategies. Objective measures of infection and exposure to pathogens, and measures of gut function, are needed to understand the effectiveness and impact of water supply improvements.Methods and analysisIn the PAASIM study, we examine the impact of water system improvements on acute and chronic health outcomes in children in a low-income urban area of Beira, Mozambique, comprising 62 sub-neighborhoods and ∼26,300 households. This prospective matched cohort study follows 548 mother-child dyads from late pregnancy through 12 months of age. Primary outcomes include measures of enteric pathogen infections, gut microbiome composition, and source drinking water microbiological quality, measured at the child’s 12 month visit. Additional outcomes include diarrhea prevalence, child growth, previous enteric pathogen exposure, child mortality, and various measures of water access and quality. Our analyses will compare a) subjects living in sub-neighborhoods with the improved water to those living in sub-neighborhoods without these improvements; and b) subjects with household water connections on their premises to those without such a connection. This study will provide critical information to understand how to optimize investments for improving child health, filling the information gap about the impact of piped water provision to low-income urban households, using novel gastrointestinal disease outcomes.Ethics and disseminationThe study was approved by the Emory University Institutional Review Board and the National Bio-Ethics Committee for Health in Mozambique. The pre-analysis is published on the Open Science Framework platform (https://osf.io/4rkn6/). Results will be shared with relevant stakeholders locally, and through publications.STRENGTHS AND LIMITATIONS OF THE STUDYThis matched cohort study of an urban water supply improvement project will provide critical information about the health impacts of providing piped water and household connections to low-income households.We employ rigorous measures of exposure and novel and objective outcome measures, including gut microbiome composition and molecular detection of enteric pathogens.The study design allows for examination of both neighborhood and household-level effects of water supply improvements.As a natural experiment, we are unable to randomize the intervention, leading to potential residual confounding.We are unable to examine the impacts of all aspects of the city-wide water improvement project, due to lack of comparable populations, and instead focus only on the low income neighborhoods.