The complexity of current socio-environmental impacts on marine and coastal ecosystems has pushed scientific endeavors toward more participative and holistic approaches, such as the Post-Normal Science, Marine Ecosystem-Based Approach and Integrated Coastal Management. Knowledge integration is a key element of these approaches. Nevertheless, the development of integrated and interdisciplinary research still faces many obstacles. Here, we discuss the process of scientific knowledge production and integration among the diverse research areas of Oceanography and between science and society. Aiming to contribute to the development of future interdisciplinary scientific research and to improve science-policy interface in coastal zones, we conducted an analysis of an oceanographic research project in which an interdisciplinary and applied approach was adopted to understand the components, processes and importance of a coastal bay in Southeast Brazil. From interviews with project researchers, a documentary analysis and a social network analysis, we showed that interdisciplinarity was stronger (a) within groups from related research fields and (b) with specific management modules. Similarly, integration between the project and society was limited to specific research modules. In addition, it was possible to identify actions that would foster integration in future research projects, related to developing common research goals, concepts and methods, such as promoting opportunities for integration and investing in publications for lay people in addition to scientific publications. Despite not achieving the objectives of interdisciplinarity and integration with every project module, the project resulted in important legacies that have impacted the Araçá Bay community and local decision-making. This project can be considered to be a good example of integrated science in Brazil, especially regarding the under-explored potential of interdisciplinarity development within oceanographic projects.