The aim of this chapter is to provide an overview of the characteristics of the principal ecosystems along the Brazilian coast, their importance in economic and social terms, the need to sustain their biodiversity, especially in the face of their main threats. In general, the Brazilian continental shelf is oligotrophic, with a predominance of tropical waters, typical of western contour systems around the world. Fertilization of coastal regions by estuarine plumes occurs in several locations, the most outstanding being that of the Amazon River, which exerts a major influence on the continental shelf and adjacent oceanic region and can be observed for many hundreds of kilometres. Among the different ecosystems, those particularly highlighted are the estuaries and mangroves, the rocky shores, the coral reefs and oceanic islands due to their great ecological, economic and/or socio-cultural importance. Additionally, there is discussion regarding the main conservation threats and challenges shared by the different marine ecosystems, such as urban/coastal development, solid waste, pollution, climate change and fishing. It is to be emphasised that there is a need to develop both basic and applied research in the different marine ecosystems and in different aspects,including, but not limited to: surveys and distribution of the biodiversity; the dynamics and functioning of the ecosystems; interaction among the organisms and with the environment as a whole; the impacts and main sources of pollution; delimitation of priority areas for conservation and promotion of conservation policies; environmental perception and education, includingmarine ecosystem awareness campaigns for the public.Estuarine ecosystems, particularly those with mangrove forests, give rise to deeply rooted economic and cultural controversy in Brazilian society. Although considered permanent protection areas, they remain listed as one of the most threatened biomes on the planet, thousands of hectares being lost every year.