The AquaINFRA Marine Modeling System is an integrated modeling workflow built around the MIT General Circulation Model (MITgcm, https://mitgcm.org). It provides a complete chain of tools for data preprocessing, model execution, and post-processing/visualization, implemented in Bash, Python, and Fortran. The preprocessing module automates the preparation of all input fields required for MITgcm simulations. In the current implementation, oceanographic initial and boundary conditions are sourced from the Copernicus Marine Service Mediterranean Sea products (CMEMS, https://marine.copernicus.eu), while atmospheric forcing is obtained from the ERA5 reanalysis via the Copernicus Climate Data Store (CDS; https://cds.climate.copernicus.eu). Additional input datasets—such as bathymetry, land–sea masks, and river discharge climatologies—are also incorporated. In the current release, the computational domain is fixed to the northwestern Mediterranean Sea; the corresponding bathymetry grid, coastline masks, and river forcings are bundled with the system. The execution module includes a fully parameterized MITgcm configuration tailored to this domain, covering grid discretization, numerical solver settings, physical parameterizations, and runtime control. Post-processing tools provide automated diagnostics, field extraction, and plotting routines to support evaluation and visualization of simulation outputs. The system is designed for seamless integration into the Galaxy platform (https://galaxyproject.org) through the AquaINFRA interoperability architecture (https://aquainfra.eu), where each component of the modeling chain is exposed as an OGC API process implemented via pyGeoAPI (https://pygeoapi.io). Within this framework, the AquaINFRA Marine Modeling System is represented as a Galaxy tool composed of three dedicated pyGeoAPI processes—corresponding to preprocessing, model execution, and post-processing. All components are deployed as Dockerized services to ensure reproducibility, interoperability, and seamless orchestration within cloud-based and distributed Galaxy environments. How to cite: Galiana, S., Buurman, M., Konkol, M. & Ballabrera-Poy, J. (2025). AquaINFRA Marine Modeling System [Software]. Zenodo. https://doi.org/10.5281/zenodo.17736641