Since the beginning of the twentieth century, observations have shown a significant degradation of aquatic environments. This degradation has got worse in the past century in all regions of the Globe. This is observed in many estuarine areas vital for the growth of high‐value species. Given the state of degradation of these coastal environments, their vulnerability to the anthropic effects and the natural hazards has become stronger whereas their resilience capacities have become significantly lower. The same goes for the many human communities living from the exploitation of living resources that can no longer ensure the sustainability of their fishing or farming activities. In addition to all these modifications the impacts, now proven, of climate change alter the temperature of water masses and biogeochemical characteristics of marine ecosystems. This integrated vision of the marine environment and of the aims of research makes it possible to address the issue of environmental governance and the problems involved in coordinating the knowledge and functions of scientific, social, economic and political actors. The three authors who are specialized in different fields of research exchange their points of view, redefine the terms, notions, concepts, and the questions related to the exercise of transdisciplinarity.