Long-term sustainable port development requires accounting for the intrinsic values of ecosystems. However, in practice, ecosystem considerations often only enter the planning and design process of ports when required by an Environmental Impact Assessment. At this late stage, most of the design is already fixed and opportunities to minimize and restore ecosystem impacts are limited. In this paper, we adopt a large-scale, ecosystem perspective on port development with the aim to identify ecosystem-based design alternatives earlier and throughout the planning and design of a port's marine infrastructure. We present a framework, termed the 'ecosystem-based port design hierarchy' (EPDH), to identify ecosystem-based alternatives at four hierarchical design levels: 1) alternatives to port developments, 2) port site selection, 3) port layout design, and 4) design of structures and materials. In applying the EPDH framework retrospectively to a case study of port expansion in Tema, Ghana, we establish that ecosystem considerations played only a limited role in identifying and evaluating alternatives at all four design levels in the case study, whereas more eco-friendly alternatives in terms of port layouts, structures, and materials are identified using the EPDH framework. This reveals that opportunities for ecosystem-friendly port designs may have been missed and demonstrates the need for and the potential added value of our framework. The framework can assist practitioners in earlier and wider identification of ecosystem-based alternatives for a port's marine infrastructure in future seaport developments and, hence, represents an important step towards more sustainable port designs.