Luanda Bay (LB) is the second largest coastal bay in Angola, located in front of Luanda city, and protected by an island. LB is a rich ecosystem that provides a wide diversity of services. Due to its relevance, multiple pressures on surroundings areas are threatening the ecosystem. Solid waste and untreated domestic effluents are released daily into the Bay, hampering the practice of nautical sports, and the subsistence of fishing and leisure activities. The government recently approved a program to rehabilitate the marginal area of LB. The prediction of the environmental responses to rehabilitation actions, and the mitigation of current threats to LB, requires the analysis of water and sediment quality and evaluation of trophic dynamics, including potential toxic species (e.g., HABs). This project will provide biodiversity databases and a deeper understanding of the determinants underlying poor water quality, specifically toxigenic species presence, in LB, in comparison to a reference site, Mussulo bay. An ecosystem-based approach, crucial for planning the future development of LB, is based on two main principles: maintaining and improving the ecosystem health, and balancing derived society values. In order to achieve these objectives, an Ecological Risk Assessment (ERA) will be developed for LB to identify priority issues and management actions. This exercise will involve relevant local and management institutions to facilitate a participatory approach so that society becomes an integral part of the project facilitated by the Collaborative Research Center in Marine Sciences “CCEMAR” that will be established. The sustainable development of the sea is a major goal of Blue Economy and Blue Society, integrating marine resources and the mitigation of environmental risks for increasing the QoL.