Although the importance of pursuing meaningful and equitable transdisciplinary research collaborations with Indigenous and local community members has been established in the literature, challenges remain as to how to best do this in practice. Pursuing arts-based participatory research methods in two different ocean governance contexts in South Africa, this paper provides reflections by social and marine scientists, Indigenous and local community members, and artists taking part in transdisciplinary collaborations as co-researchers and co-facilitators. Centralizing the use of arts-based methods in the form of storytelling and photography, we consider some key lessons emerging from this transdisciplinary research for transformative ocean governance. This includes the need to actively critique and disrupt the invented roles of “researchers” and “research participants” and to build strong relationships and trust prior to the envisioned research process. We argue that the use of arts-based participatory methods has supported meaningful learning across multiple ways of relating to and connecting with the ocean and highlight inherent barriers to truly collaborative transdisciplinary research that are relevant for projects in different contexts and at various scales, such as the inequity of academic publishing processes and ownership of knowledge outputs. Despite continuous difficulties in ensuring equitable valuation of various knowledge systems, we find that arts-based participatory processes are valuable in advancing what we refer to as “comprehensive transdisciplinarity,” where non-academic co-researchers take part in conceptualization, methods formation, and dissemination of the research. We propose some critical questions that can assist teams considering transdisciplinary collaborations and conclude with some lessons and recommendations for academic institutions to better support equitable transdisciplinary collaborations that are needed to advance deep transformations toward sustainability.