Electrochemical energy storage technologies play a key role in wide adoption of electric waterborne transport systems. Currently, lithium-ion (Li-ion) is the leading battery technology in electric and hybrid maritime applications. However, specific operational requirements such as power peaks and long sailing distances remain a concern with respect to typical Li-ion batteries, mainly due to the limitations in terms of energy and power density as well as safety. While batteries used in most of marine applications are based on established Li-ion technologies, other mature storage technologies such as supercapacitors could be suitable for waterborne applications. Additionally, the next generation battery technologies such as solid-state batteries show promise for addressing some limitations of Li-ion batteries. These alternative technologies have the potential to transform the landscape of electric marine transport systems. Focusing on waterborne transport systems, this paper provides a review and a comparative analysis of common Li-ion batteries. Additionally, the alternative electrochemical energy storage technologies including supercapacitor and solid-state batteries are investigated and compared to Li-ion batteries. This research provides valuable insights into the advancements and prospects of electrochemical energy storage system for waterborne transport systems.