<p>The Amazon region relies heavily on river transportation for economic development. Thousands of passengers and cargo are transported annually through its rivers, highlighting the need for efficient vessel designs. This study contributes to decarbonization efforts by optimizing propulsion systems for displacement vessels operating in environmentally sensitive inland waterways. Using the Holtrop and Mennen method, enhanced with corrections for river depth and margin effects, the study selects and adjusts the propeller system to suit variable conditions. The methodology was applied to a regional ferryboat navigating the Manaus–Tabatinga route on the Solimões River. The results show that shallow waters can increase resistance by up to 14%, while river margins add an additional 6%. The proposed optimization not only improves operational efficiency but also reduces fuel consumption and emissions, aligning with sustainable practices. Additionally, the propulsion system was designed to meet critical shallow water navigation conditions during the dry season, while allowing operational adjustments to maximize efficiency in deep waters during the rainy season. This approach reinforces the role of the developed computational tool in advancing propulsion systems for inland waterways, promoting more efficient and sustainable navigation in the Brazilian Amazon.</p>