<p>Through their time at sea professional fishers possess and obtain invaluable knowledge and insights into the behaviour, distribution, and abundance of both target and non-target species. Their observations through direct experience, can offer nuanced perspectives to complement fisheries assessments, contributing to a more holistic understanding of fish behaviour, distribution and habitat use. The rivers and coastal regions of the Northern Territory (NT), Australia, are recognised as biodiversity hotspots, providing critical habitats for several threatened, endangered and protected species (TEPS), including Sawfish (<i>Pristis</i> spp.) and River Sharks (<i>Glyphis</i> spp.). The limited information available on the population sizes and distribution for these species hinders the development of comprehensive management plans. Reported interactions with these species occur within several NT commercial fisheries. Here we document professional fishers’ knowledge on historical and current interactions with Sawfish and River Shark species across several commercial fisheries. We present the findings from 16 semi-structured fisher interviews and mapping activities with fishers including spatial and temporal patterns of interactions, species associations, and potential mitigation measures. The findings contribute knowledge that qualify and record the evolving attitude of fishers towards species interactions, and provides insights that can guide future management strategies, whilst also building relationships between professional fishers, researchers, industry and fishery managers. Providing opportunities for professional fishers to share their knowledge and participate in management decisions about protecting threatened species caught incidentally in fishing operations is seen as crucial area for the fishing industry to support and to ensure sustainability of commercial fishing livelihoods.</p>