The subject of ecology is the understanding of the relations among living organisms and their interactions with the abiotic environment. The need to quantify ecological phenomena requires the development of mathematical tools, including ecological indices, statistical procedures and simulation models. Some of these tools have been found to be convenient by many scientists and policy makers in related scientific disciplines to express marine pollution levels, marine water quality and future trends; they have, therefore, been adopted in coastal management methodologies and practices. In the present work, a number of ecological tools are reviewed regarding their relevance to supporting water quality studies, as well as their suitability to be included in the toolkit of coastal management practices. Their problems and weaknesses, together with the science–policy misconnection, are discussed.

The role of coastal marine ecosystems, especially saltmarshes, seagrass beds, and mangroves, has been substantial in mitigating climate change due to carbon sequestration. In particular, coastal eutrophic systems characterized by dense phytoplankton communities could be substantial contributors, as they retain significant amounts of carbon in organic form, representing, therefore, an important ecosystem service. However, the quantification of the contribution of phytoplankton in such a process is constrained by methodological gaps and uncertainties. In this paper, a stepwise procedure is presented to assess the carbon retained by phytoplankton in a coastal eutrophic system, and methodological limitations are discussed. The authors suggest that the contribution of phytoplankton in coastal eutrophic systems should be quantified and considered in the Blue Carbon balance within climate change mitigation frameworks.