The speartooth shark Glyphis glyphis is a Critically Endangered whaler shark. Strong female philopatry results in genetically isolated populations of juveniles that are restricted to less than 10 tropical estuaries across northern Australia. Acoustic telemetry has shown restricted movement of juveniles in rivers and estuaries related to annual wet season flows. In the Wenlock and Ducie River, Queensland, juveniles have specific habitat preferences and are confined to a 20-40 km stretch of river with downstream movement associated with reduced salinity/freshwater flows. Using close kin mark recapture, the adult female population that pup in the Wenlock and Ducie River was estimated at 100 individuals that give birth to around 500-600 pups annually. Bycatch of juvenile speartooth sharks in a commercial mud crab fishery was identified as a threat to the population in the Wenlock and Ducie River. We worked with commercial fishers to obtain data on catch rates of speartooth sharks in crab pots and test the efficacy of shark excluders at reducing bycatch of sharks in crab pots. The effect of spatial closures at reducing bycatch of speartooth sharks was also investigated. Shark excluders resulted in a 98 % reduction in catch rates of speartooth sharks and a 14 % reduction in catch rates of legal-size mud crabs. Seasonal and permanent spatial closures of critical habitat reduce speartooth shark bycatch by 10 and 68%, respectively and resulted in 4 and 7 % reduction in crab catches. Population modelling was used to explore whether current bycatch rates are resulting in population declines and what level of bycatch (fishing mortality) will result in population growth.