Numerical simulation plays a critical role in environmental assessment, planning, and management and is widely used to evaluate the aquatic environmental impacts of port construction in coastal and estuarine areas. For evidence-based policymaking, it is highly advantageous to provide systems that enable users with little or no experience in numerical modeling to easily perform simulations. In particular, for engineers unfamiliar with computer operations, a simulation environment based on a graphical user interface (GUI), rather than a command-line interface, is essential. Our research group developed the EcoPARI-Web GUI (Matsuzaki et al., 2024), a web-based application designed to support performing hydrodynamic and ecosystem simulations using the EcoPARI-Simulator as the solver (Tanaka and Suzuki, 2010; Tanaka et al., 2011). This system integrates pre-processing (creation of computational conditions) and post-processing (visualization of simulation results) into a single platform. These processes typically impose the greatest workload in aquatic environment simulations, and a web-based implementation is expected to significantly improve efficiency and accessibility. Despite these advancements, two major challenges remain: the execution of simulations and the validation of their accuracy. Traditionally, users were required to build computational servers and compile numerical models, whereas accuracy verification required visualization and statistical analysis of observational data—tasks that are often difficult for non-specialists. To address these issues, we are developing an integrated system that enables web-based execution on supercomputers managed by Osaka University and the University of Tokyo (SQUID, Wisteria/BDEC-01, mdx) and supports visualization and statistical analysis using pre-stored observational data. Once completed, this end-to-end aquatic environment simulation system will enable seamless comparison between simulations and observations, functioning as a form of digital twin technology. This development is expected to significantly advance research and practical applications in environmental modeling and management.