The Organic Rankine Cycle (ORC) is one of the most promising systems to recover the waste heat sourced from internal combustion engines. In this study, thermodynamic, economic and environmental analyses of the scavenge air cooling water-driven Waste Heat Recovery System (WHRS) based on the organic Rankine cycle are conducted for a dual-fuel marine engine integrated with exhaust gas recirculation (EGR) system. Zero ozone-depleting and low global warming potential working fluids; R245fa, R236ea from hydrofluorocarbons, R600a, R601a from hydrocarbons, R1234ze and R1234yf from hydrofluoroolefins are selected for the low-grade WHRS. In addition to the thermal analyses, the mass and volume of the system along with the safety factors of the working fluids are evaluated to judge the physical applicability of the system for ships. Thermo-economic performances of the fluids are analyzed, optimized and compared under various engine loads, Tier II and Tier III modes to reveal the effects of different engine operating conditions on the parameters. According to the results, scavenge air has a significant amount of waste heat at medium and heavy loads and switching the engine mode remarkably affects the performance of the WHRS. R601a shows the best thermo-economic performance, however, considering the applicability of the system R236ea is the most suitable working fluid for the ORC WHRS. The overall thermal efficiency of the power generation system can be increased by about 2.8%.