In Queensland, commercial trawl fisheries and protected marine species share dynamic environments where ecological and anthropogenic activities intersect. Understanding where these interactions occur is fundamental to developing management strategies that support both ecosystem conservation and sustainable fisheries. We developed habitat suitability models for sea snakes incidentally caught in the Great Barrier Reef Marine Park and integrated these with commercial trawl fishing effort to locate areas of elevated bycatch risk. Habitat suitability was predicted using environmental variables and occurrence records, before being overlaid with spatial fishing effort data to quantify areas of potential interaction. We identified key areas of elevated bycatch risk in the marine park where high-quality habitat coincided with historically intensive trawling activity. These findings highlight opportunities for targeted monitoring and mitigation and demonstrate how spatial modelling can inform adaptive management of shared marine ecosystems.