The decarbonization problem of maritime transport and new restrictions on CO2 emissions (MARPOL Annex VI Chapter 4, COM (2021)562) have prompted the development and practical implementation of new decarbonization solutions. One of them, along with the use of renewable fuels, is the waste heat recovery of secondary heat sources from a ship’s main engine, whose energy potential reaches 45–55%. The organic Rankine cycle (ORC), which uses low-boiling organic working fluids, is considered one of the most promising and energy-efficient solutions for ship conditions. However, there remains uncertainty when choosing a rational cycle configuration, taking into account the energy consumption efficiency indicators of various low-temperature (cylinder cooling jacket and scavenging air cooling) and high-temperature (exhaust gas) secondary heat source combinations while the engine operates within the operational load range. It is also rational, especially at the initial stage, to evaluate possible constraints of ship technological systems for ORC implementation on the ship. The numerical investigation of these practical aspects of ORC applicability was conducted with widely used marine medium-speed diesel engines, such as the Wartsila 12V46F. Comprehensive waste heat recovery of all secondary heat sources in ORC provides a potential increase in the energy efficiency of the main engine by 13.5% to 21% in the engine load range of 100% to 25% of nominal power, while individual heat sources only achieve 3% to 8%. The average increase in energy efficiency over the operating cycle according to test cycles for the type approval engines ranges from 8% to 15% compared to 3% to 6.5%. From a practical implementation perspective, the most attractive potential for energy recovery is from the scavenging air cooling system, which, both separately (5% compared to 6.5% during the engine’s operating cycle) and in conjunction with other WHR sources, approaches the highest level of exhaust gas potential. The choice of a rational ORC structure for WHR composition allowed for achieving a waste heat recovery system energy efficiency coefficient of 15%. Based on the studied experimental and analytical relationships between the ORC (generated mechanical energy) energy performance (Pturb) and the technological constraints of shipboard systems (Gw), ranges for the use of secondary heat sources in diesel operational characteristic modes have been identified according to technological limits.