Remote, data-limited marine environments are poorly understood, making conservation and resource management major challenges in the rapidly changing environment. High field data collection costs results in sparse data, which limits the traditional scientific approach to understand the functioning of these remote ecosystems. The Gulf of Carpentaria is a vast, remote and data-limited region in northern Australia that is vulnerable to rapid changes due to climate change and externally derived marine debris, but extremely difficult and costly to access. This study aimed to test a method of improving certainty in ecological and physical processes in the Gulf of Carpentaria by maximising the use of alternative biophysical data from local Indigenous-owned and managed land and sea country, to elucidate the ecosystem functioning. We investigated the role of currents and wind in previously published Green turtle (Chelonia mydas) post-nesting satellite tracking migration data, and found they had no influence on the turtles' migration path. We also found that turtles did not use compass bearing alone to make their migration, rather they seemingly used coastal cues to 'leap-frog' along the coastline until they reached their foraging grounds. Next, we identified the spatio-temporal distribution of floating marine plastics using Indigenous-lead citizen science coastal marine debris surveys, and found that previous studies have underestimated marine debris presence in the region. Finally, biophysical modelling suggests that large migrations (>200 km in 28–35 days) of tagged male Giant mud crabs (Scylla serrata) against prevailing winds, currents and tides were possible by using selective tidal stream transport and directional swimming. These case-studies demonstrate the effectiveness of explorative biophysical modelling supported by alternative field data, and improve certainty in ecological processes with significance in culture, conservation and commercial values in the region.