Located in the center of the largest river basin in the world, the State of Amazonas in Brazil has an extensive network of more than 20 thousand kilometers of navigable waterways, which is the main mode of transportation between localities, both for cargo and passengers. The region is practically disconnected from the rest of the country due to the lack of roads. Thus, the Amazon River network acted as an efficient means of transmission of the new coronavirus (COVID-19), rapidly transforming the region into an epicenter of the pandemic with one of the highest infection rates in Brazil. Despite the adoption of national and state measures to combat new infections, the situation continued to deteriorate for reasons still under investigation. Given this scenario, this work aims to identify possible infection risks in typical passenger vessels used in the Brazilian Amazon. Three case studies of different passenger vessels were considered, discussing possible scenarios that could allow the spread of COVID and proposing some recommendations for infection prevention. It is hoped that this communication will contribute to the dissemination of information related to the typical means of long-distance passenger transport in the Amazon, to the planning of infectious disease prevention strategies on board regional ships and to ensure a sustainable future for the Amazonian population. Furthermore, this research aims to contribute to the sustainable development goals of the United Nations 2030 Agenda on health and well-being.