Growing awareness of the role of marine spatial planning (MSP) in promoting sustainable development and ecosystem-based management highlights the need to use decision-support tools, and specifically ecological modelling tools, to consider the future impact of planning and management on the marine environment. However, how these tools can be incorporated into planning and their expected contribution is not always clear. Here, an Ecopath with Ecosim and Ecospace food-web model was used in a hypothetical planning process to examine the integration of food-web tools in specific stages of MSP. The model was used to examine spatial alternatives and management strategies for Orot Rabin coastal infrastructure facility in the Israeli Mediterranean coast, in an attempt to assess how such facilities might promote marine conservation. The results revealed the effect of different management protocols on the ecosystem, and provide the maximum allowable catch for sustaining the biomass of vulnerable fish species in the area, which can be used in MSP to address specific marine conservation goals. The model led to counterintuitive understandings regarding the management of the area. It demonstrated that intensive development under specific management strategies may promote conservation goals better than some management strategies directed towards ecological and recreational purposes. This study confirms the potential usefulness of food-web models for MSP; it specifies the stages and means by which planners can use models. Furthermore, it is suggested that tool's development should be planning-oriented and should include more applications to serve planners who aim to promote ecosystem-based management and marine conservation goals.