While the development of stability regulations mainly has been driven by the needs for passenger ships, cargo ships are also getting an update in the newly adopted amendments to the Safety of Life at Sea (SOLAS) convention. The stability at intermediate flooding stages have previously been ignored for cargo ships, but if the ship is equipped with cross-flooding devices, intermediate filling phases will now be evaluated. In this study, the relevancy of these intermediate stages for cargo ships is investigated. The focus is on a case study of a short sea ro-ro cargo ship with cross-flooding ducts in the double bottom. In addition to the conventional regulatory calculation methods, also time-domain flooding simulation is used for realistic assessment of intermediate stages and the actual time-to-flood. Such tools have previously been used for damage stability analyses of passenger ships. The different calculation methods are compared against each other through the attained subdivision index. The results indicate that cross-flooding improves damage stability also for cargo ships, and that simulation is an applicable tool also for design and analysis of safer ships.