• A distribution network integrating urban waterways and last-mile delivery, exemplified by Amsterdam. • A novel two-echelon location routing model and an efficient hybrid solution approach. • Results demonstrating substantial cost savings and enhanced infrastructure lifetime. • A significant emission reduction, highlighting the potential for greener urban logistics. • Extending beyond Amsterdam, with guidance for cities to promote sustainable urban logistics. This paper tackles the growing challenges in urban logistics by presenting an optimal distribution network that integrates urban waterways and last-mile delivery, tailored for cities boasting extensive waterway networks. We examine Amsterdam's city center as a case study, prompted by the strain on quay walls, congestion, and emissions, urging a reevaluation of its urban logistics design. We formulate the problem as a two-echelon location routing problem with time windows and introduce a hybrid solution approach for effective resolution. Our algorithm consistently outperforms existing methods, with a superior solution quality, demonstrating its effectiveness across established and newly developed benchmark instances. In our case study, we evaluate the benefits of transitioning from a roadway-centric to a waterway-based system, showcasing significant cost savings (approximately 28 %), reductions in vehicle weight (approximately 43 %), and minimized travel distances (approximately 80 %) within the city center. The integration of electric vehicles enhances environmental sustainability, resulting in a total daily emission reduction of 43.46 kg. Our study underscores the untapped potential of inland waterways in easing urban logistics challenges. Inspired by Amsterdam's experience, global cities can adopt innovative approaches for sustainable logistics, providing valuable insights for managers striving to enhance efficiency, cut costs, and promote sustainable transportation practices. [ABSTRACT FROM AUTHOR]