The urgent need to reduce energy consumption and environmental impact in the shipping industry has prompted research and industry to explore new solutions for minimizing fuel usage. This study examines the potential effects and benefits of integrating electrical energy storage systems, such as lithium-ion batteries and supercapacitors, into short sea shipping ships during port stay. Specifically, a novel dynamic simulation tool is developed to conduct suitable analyses that investigate the feasibility of charging electrical storage systems while at navigation and utilizing them as alternatives to traditional diesel generators while in port. The analysis reveals that lithium-ion batteries and supercapacitors are effective tools for reducing pollutant emissions by minimizing diesel generator usage during port stopovers, resulting in a significant reduction in fuel consumption from 1.148 kt/year to 0.511 kt/year. Moreover, under identical conditions, the use of supercapacitors increases the lifespan of batteries from 10.6 years to 11.9 years. Additionally, there is a 55 % reduction in carbon dioxide emissions during port stays, decreasing from 2.98 kt/year to 1.64 kt/year.