Recognition of the need for marine research that spans the social-ecological divide has opened an exciting space for transdisciplinary research. Yet, attempts at working across disciplines often leads to epistemological debates and methodological rifts between natural and social sciences, presenting significant challenges for transdisciplinary teams. Using fisheries research within the context of a coral reef social-ecological system as a case study, we explore how these points of tension may be addressed using a three stage process: 1) promoting epistemological transparency, where differing perspectives are made explicit; 2) employing feedbacks as a bridging concept to effectively engage with complex system dynamics from multiple perspectives; and 3) encouraging plurality, rather than the unification of perspectives, to foster innovative research along sustainable and desirable pathways.