Auxiliary drives can provide an alternative propulsion system for marine vessels giving the potential to achieve improved environmental performance during low-speed sailing. In this work, two case vessels were considered for analysis, a Roll-On–Roll-Off ship and a harbour tug boat. Actual sailing operational profiles were used as the basis for energy considerations to assess the potential for lower emissions. An energy-centric simulation model was built to estimate the emission of various pollutants, considering different machinery set-ups. Results have shown that savings are possible, especially for vessels which run on residual fuels, where auxiliary drives provide a way of exploiting the advantages of cleaner sources for manoeuvring instances.