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This study examines the optimal sizing of an energy storage system (ESS) to reduce hazardous pollutant emissions in a series hybrid powertrain designed to replace conventional waterbuses in Venice. The proposed system consists of three generator sets and two electric motors, offering a cleaner alternative for the city’s public transportation network. A quasi-static simulation model was developed to assess powertrain performance using real-world operational data collected from waterbuses operating in the Venice Lagoon. Dynamic programming was employed to derive emissions-optimal control strategies, minimizing the trade-off between nitrogen oxides (NOx) and hydrocarbons (HC). By simulating different ESS configurations, the study assesses how energy storage capacity influences emissions reduction potential and system flexibility. At the same time, using the optimal energy management strategy when comparing different ESS sizes ensures that each configuration operates under the best possible conditions, eliminating biases introduced by suboptimal control strategies. This approach isolates the impact of ESS capacity on emissions and performance, allowing for a fair comparison between different storage sizes. The results indicate that even a relatively small ESS can significantly reduce NOx and HC emissions, while a larger ESS provides greater flexibility in selectively mitigating specific pollutants. Additionally, a larger ESS enables pure electric operation, allowing emissions to be spatially shifted when necessary. These findings emphasize the potential benefits of hybrid-electric ferries for coastal cities. Retrofitting existing fleets and integrating hybrid technologies into new vessels could play a critical role in improving urban air quality, ensuring compliance with emissions regulations, and advancing sustainable maritime transport.