Several studies on the pathophysiological and epidemiological characteristics of SARS-CoV-2 indicate the extracorporeal viability of the virus and the possibility of faecal-oral transmission through contaminated natural water and wastewater, suggesting a potential risk of spreading in socially vulnerable areas, such as the Brazilian Amazon, where access to sanitation and health services is lacking. Thus, an attempt we made to outline an overview of sanitation in the Brazilian Amazon and its possible impacts on the most vulnerable populations and on the health system in a pandemic situation, based on bibliographic and documentary review and exploratory analysis of data related to basic sanitation and health. The Amazon has a huge deficit in sanitation and in the structure of health services, especially in rural areas, increasing the risk of spreading infectious diseases such as COVID-19, whose progress has placed some of the Amazonian states in a prominent position in the rankings of incidence and mortality.