Precise accounting of ecological assets plays a fundamental role in facilitating interregional ecological compensation and advancing green development practices. By adopting the entire aquatic ecosystem as the compilation object and incorporating the value of aquatic products and aquatic ecosystem services into the measurement scope, this study explores the development of a water ecological balance sheet. Using relevant data from Changzhou from 2022 to 2023 as a sample, the application of the regional water ecological balance sheet is validated. The study reveals: Establishing a capital reserve account creates interlinkages between balance sheet items, forming a “Chango Table-Master Table” reporting system that enables systematic monitoring and dynamic assessment of regional water ecological assets, liabilities, and equity. The compilation principles of “quantifying physical quantities before monetary values, and classifying before synthesizing” can effectively reflect the adaptability of local governments’ water ecological policy management. The compilation method clearly reveals changes in Changzhou’s water ecological asset structure and their driving factors. It accurately captures resource and environmental shifts under Changzhou’s water ecological policy interventions, thereby providing reliable evidence for evaluating ecological protection policy effectiveness and supporting water ecological management decisions.