Biodiversity assessments by research scientists are often logistically difficult and expensive to implement in remote areas. Locally-based approaches have the potential to overcome some of these challenges by capitalising on the knowledge and capacity of local people. Many Indigenous people in northern Australia are custodians of coastal areas that support globally significant populations of tropical marine mammals, including coastal dolphins and dugongs. The objective of our study was to design and implement a locally-based approach in a cross-cultural environment to assess the distribution of marine mammals in the remote waters of the Gulf of Carpentaria, Northern Territory. The study was conducted as a partnership between Yanyuwa Aboriginal families, research scientists, government officers and the li-Anthawirriyarra Sea Rangers. We conducted a series of participatory mapping workshops to share and record local observations of dolphins and dugongs. These observations provided the longitudinal information required to inform the design of the first dedicated marine mammal vessel survey in the Gulf of Carpentaria. The vessel surveys found three species of dolphins present in the area (Australian snubfin, humpback and bottlenose dolphins), even though sightings were low; dugongs being much more common. We found that the integrative and locally-based approach built the capacity of both the li-Anthawirriyarra Sea Rangers and research scientists to assess the distribution of marine mammals. If replicated over longer time-frames and coordinated over broader spatial scales, information on distribution and abundance derived from locally-based approaches has the potential to inform the status of marine mammals.