The city of Amsterdam is facing various challenges in managing urban freight transport within its historic and densely populated inner city. With a rapidly growing population and increasing number of trips to, from, and within the city, Amsterdam is facing pressure on accessibility, road safety and quality of life. Furthermore, Amsterdam needs to renovate a significant portion of its historical quays and bridges, which will have a major impact on urban freight transport. The city’s commitment to maintaining accessibility and liveability, combined with its ambitious goals, has led to advancements in urban freight transport, with one notable initiative being waterborne transport. While many initiatives of waterborne transport showed success in pilot projects and demonstrations, large-scale or long-term implementation could give rise to unexpected side effects. Challenges also persist due to government policies and the cooperation of key stakeholders. In this research a design methodology is presented for sustainable urban waterborne freight distribution. The design methodology offers a stepwise approach for designing, evaluating, and generating implementation guidance for waterborne freight transport, enabling a thorough understanding and assessment of impacts. The design methodology is applied to the case study of het Wallengebied of Amsterdam. During these steps, several alternatives were prepared and scored for all stakeholders involved based on the criteria important to them. Possibilities to turn certain alternatives with a poor score on a criterion into a more positive score were considered to improve its potential in designing sustainable urban waterborne freight distribution.