Underwater exhaust systems are employed on board ships to allow zero direct emissions to the atmosphere with the possibility of drag reduction via exhaust gas lubrication. However, underwater expulsion of exhaust gases imparts high and dynamic back pressure, which can fluctuate in amplitude and time period as a ship operates in varying sea-states depending on its geographical location and weather conditions. Therefore, this research aims to experimentally investigate the performance of a marine diesel engine against varying amplitudes and time periods of dynamic back pressure at different sea-states due to underwater exhaust systems. In this study, a turbocharged, marine diesel engine was tested at different loads along the propeller curve against dynamic back pressure waves produced by controlling an electronic butterfly valve placed in the exhaust line after the turbine outlet. Engine performance was investigated against single and multiple back pressure waves of varying amplitudes and wave periods based on real sea-state conditions and wave data. We found that the adverse effects of dynamic back pressure on engine performance were less severe than those found against static back pressure. Governor control and turbocharger dynamics play an important role in keeping the fuel penalty and thermal loading low against dynamic back pressure. Therefore, a marine engine may be able to handle much higher levels of dynamic back pressures when operating with underwater exhaust systems in higher sea-states.