Abstract The transient performance of a direct-drive large two-stroke marine diesel engine, installed in a vessel operating in a seaway with heavy weather, is investigated via simulation. The main engine of the ship is equipped with a selective catalytic reduction (SCR) aftertreatment system for compliance with the latest International Maritime Organization (IMO) rules for NOx reduction, IMO Tier III. Because of limitations of exhaust gas temperature at the inlet of SCR systems and the low temperature exhaust gases produced by marine diesel engines, in marine applications, the SCR system is installed on the high-pressure side of the turbine. When a ship sails in heavy weather, it experiences a resistance increase, wave-induced motions, and a time-varying flow field in the propeller, induced by ship motions. This results in a fluctuation of the propeller torque demand and, thus, a fluctuation in engine power and exhaust gas temperature, which can affect engine and SCR performance. To investigate this phenomenon and take into account the engine–propeller interaction, the entire propulsion plant was modeled, namely, the slow-speed diesel propulsion engine, the high-pressure SCR system, the directly driven propeller, and the ship’s hull. To simulate the transient propeller torque demand, a propeller model was used, and torque variations due to ship motions were taken into account. Ship motions in waves and wave-added resistance were calculated for regular and irregular waves using a 3D panel code. The coupled model was validated against available measured data from a shipboard propulsion system in good weather conditions. The model was then used to simulate the behavior of a Tier III marine propulsion plant during acceleration from low to medium load, in the presence of regular and irregular waves. The effect of the time-varying propeller demand on the engine and the SCR system was investigated. Introduction The effect of waves on a marine propulsion system is a complex phenomenon involving interactions between different subsystems of the propulsion plant, i.e., the prime mover, the propeller, and the ship’s hull. Ships sailing in heavy weather conditions experience a resistance increase, wave-induced motions, and a time-varying flow field in the propeller. This leads to a fluctuation of the propeller torque demand which results in a fluctuation in engine-produced power and exhaust gas temperature.