Ecological areas visits require appropriate management of key ecological features. In protected reserves innovative systems should be developed to facing problems of pollution, exhaust fumes and noise. These underlying conditions lead to special challenges for excursions ships. The switching to a cleaner, safer and quieter transport system seems to be a sustainable long-term solution for the problems of ecological areas, where more electric ship can be an important part of the solution and principally for the last mile. This paper presents a design approach of a hybrid Energy Storage Systems (ESS) for new generation of series hybrid excursion ship devoted to ecological areas to avoid any emission during the casting-off and the docking maneuvers. The main purpose of the paper is to show that, even if the hybrid ESS plus series-hybrid propulsion were already used to other vehicles, the gain for a ship with no regenerative capability is not evident. The proposed hybridization is built upon a fully-active parallel topology with battery and supercapacitors. The sizing methodology and the configuration of the ESS are detailed. For a real mission profile in Alster Lake (Hamburg, Germany) it is shown that a small battery pack of 2 kWh with a supercapacitor bank of 0.54 kWh are necessary to have zero-emission maneuvers. The graphical formalism Energetic Macroscopic Representation (EMR) is used to describe the model and to establish an energy analysis tool. An inversion-based control scheme is then deduced from the EMR and simulation results are provided to validate the proposed methodology. The usage of hybrid ESS avoids 1.39 kg of CO2 during the casting-off and docking maneuvers despite increasing consumption of 0.2 l (+8%). However, the plug-in capability can be introduced and a recharge of the battery when the ship is docked could reduce the global consumption and emissions by 20% in comparison to the original ship.