In this contribution, the evolution of the Bay of Brest ecosystem over the past 50 years is used to explore the construction of interdisciplinary knowledge and raise key questions that now need to be tackled at the science-policy-communities interface. The Bay of Brest is subject to a combination of several aspects of global change, including excessive nutrient inputs from watersheds and the proliferation of invasive species. These perturbations strongly interact, affecting positively or negatively the ecosystem functioning, with important impacts on human activities. We first relate a cascade of events over these five decades, linking farming activities, N and Si biogeochemical cycles, the proliferation of an exotic benthic suspension feeder, the Great scallop fishing and biodiversity in maerl beds. This cascade leads to today’s situation where toxic phytoplankton blooms become recurrent in the Bay, preventing the fishery of the great scallop and leading the fishermen community to switch pray and alter the maerl habitat and the benthic biodiversity it hosts, despite the many scientific alerts and the protection of this habitat, How is this possible despite decades of joint work between scientists and fishermen? Is adaptive co-management a sufficient condition for a sustainable management of an ecosystem? How do the different groups (farmers, fishermen, scientists, environmentalists…), with their diverse interests, take charge of this situation? What is the role of power in this difficult transformation to sustainability? Answering these questions requires an interdisciplinary approach, especially between natural sciences (NS) and human and social sciences (HSS). Here, we first show the importance of geographical proximity in the build-up of this interdisciplinary knowledge, first among biogeochemists and benthic biologists by the time the IUEM institute was built in the late 1990’s. We also confirm the importance of this proximity and the need for the establishment of boundary settings that allow for the crucially needed long-term interactions between the NS and HSS communities. The creation of the research group ApoliMer (for a political anthropology of the sea) in 2014 and the creation of a new axis on social-ecological systems (SES) within the LabexMer in 2015, are such examples of these boundary settings created recently. Combining natural sciences with political science, anthropology and the political sociology of science, we hope to improve the contribution of HSS to SES studies, creating the conditions to address these key questions at the science-policy interface. The ZABrI created in 2012 provides an ideal setting for inter- and trans-disciplinary studies through tight work with various stakeholders, hopefully improving the transformation towards sustainability.