This project presents a comprehensive study on the development of Integrated Water and Land-based Transportation (IWLT) Systems for city logistics. The research addresses the growing challenges of urban traffic by proposing a decision model for multi-modal transportation systems that leverages waterways alongside traditional road networks. The problem is defined as a two-echelon multi-trip location routing problem with satellite synchronisation (2E-MTLRP-SS), incorporating capacitated vehicles, multiple depots and time constraints. A decomposition-based decision model is introduced, breaking down the problem into manageable sub-problems interconnected through synchronisation in time, space, and load. The decision model uses metaheuristics to be able to handle large-scale, realistic problems and provide feasible solutions for real-life applications. The model’s effectiveness is demonstrated through a case study in Amsterdam, showing the potential of IWLT systems to reduce congestion-related issues and improve the livability of cities. Different scenarios for the IWLT system are investigated, to assist Amsterdam's system developers in making design choices for implementation. The proposed decision model is widely applicable to multi-modal transportation systems all over the world.