Effective conservation management combines information obtained from formal scientific research with traditional knowledge derived from communities living within the ecosystem, in an integrated and comprehensive ecosystem assessment. To complement national efforts to establish Marine Protected Areas (MPAs) in critical coastal ecosystems to protect nursery areas and spawning grounds in Ghana, two communities in the Greater Cape Three Points area in the Western Region of Ghana were involved in a participatory mapping and assessment exercise as part of an ecosystem-based approach to the establishment of MPAs in the area. The paper presents the processes by which the communities were engaged in identifying and mapping out top five priority ecosystem services (ES) vital for fisheries—an important livelihood source in the area—valuing the prioritized ecosystem services, and identifying and assessing four main anthropogenic pressures threatening the continual provisioning of ecosystem services. The relevance of such community participatory assessment in policy formulation is also discussed in the paper. The paper demonstrates that the livelihoods of rural coastal communities are linked to broader ecosystem functioning. It also shows that when participatory mapping is complemented with perspectives from direct beneficiaries of ES, managers are afforded a holistic insight into the array of issues that feed into a comprehensive management approach which addresses social, economic and ecological concerns.