Abstract Background Basic sanitation could be a potential indicator of the spread of coronavirus disease-2019 (COVID-19) and, in this context, space-time patterns are important tools with which to elucidate the spread of disease and identify risk factors. The aim of this study was to assess a possible association between basic sanitation indices and COVID-19 rates in all the 5570 municipalities of Brazil and its spatial distribution. Methods Data of COVID-19 cases registered in Brazil from 28 February until 31 May 2020 and independent variables associated with basic sanitation were included. Results High incidence rates were significantly associated with precarious water service index (0–25% coverage) and offstandard faecal coliforms index for tap water (5–50% and 75–100% of samples tested). A significant association between high mortality rates and sewage collection (0–25% coverage)/treatment (25–50% coverage) indices was also verified. In addition, clusters with significant spatial autocorrelation were identified mainly in the North and Northeast regions for mortality and incidence rates (high-high risk areas) and for offstandard faecal coliforms index. Those regions are considered the poorest in Brazil, presenting with low incomes, human agglomerations, as well as a poor basic sanitation system, which also hinder the implementation of COVID-19-preventative measures. Conclusions A precarious basic sanitation infrastructure could potentially be associated with the high transmission of severe acute respiratory syndrome coronavirus-2 in Brazil.