Faults in the prime mover of a ship would lead to unpleasant consequences during navigation, especially in the event of bad weather. To avoid troublesome situations, any faults in the propulsive chain should be promptly recognized, by observing the initial degradation of sensitive mechanical components through condition monitoring techniques. However, the effects of such degradations need to be distinguished from the offset induced by the wave actions on a healthy system. This paper concerns the analysis of the consequences of several types of degradations on a ship sailing in rough weather. The study is carried out by means of a numerical simulation model that accounts for the hull, propeller and engine interactions in irregular head seas. The degradation levels of some relevant engine components are systematically modeled and simulated. The performances of hull dynamics, propeller actions, and engine performances are monitored and compared with the healthy propulsion system, aiming at providing a correlation between cause and effect. To this end, a twin screw Ropax vessel, powered by two marine diesel engines, is considered.