Limited navigation depth, especially on inland waterways, is one of the main limiting factors that shorten the navigation period. Distributed propulsion systems represent an opportunity to increase the navigability of ships across critical sections of waterways characterized by limited navigation depth. In the case of distributed propulsion systems, it is necessary to examine the position of the propellers and their efficiency, suitable design, and interaction with the surroundings. In this study, self-propelled propulsion units located on the side of the ship are investigated at the level of computational fluid dynamics (CFD) analyses. Seven different types of ducts are considered for the proposed propeller geometry in order to ensure the necessary water supply, to prevent air intake, and to ensure high performance in the serial arrangement of propulsors on the side of the hull. Comparative analyses have shown that propulsion units with Ducts 5 and 6 have sufficient resistance to ventilation at a limited depth and deliver acceptable performance at low inflow and outflow rates. This feature is important in serial configurations, which confirms previous research on this issue. Performance can be further increased by reducing the duct resistance at higher speeds.