A recent risk assessment identified that bycatch of the threatened Australian sea lion in the Commonwealth managed demersal gillnet sector of the Southern and Eastern Scalefish and Shark Fishery in South Australia, was likely posing a significant threat to many of the small subpopulations of the species. Given that there are limited options for gear-modification in this sector of the fishery, spatial management of catch and effort provides the only practical and immediate means for reducing risks to sea lion subpopulations. In response to this, we have developed models that enable the outcomes of different spatial distributions of fishing effort and the consequential risk-reduction benefits to individual sea lion subpopulations to be estimated. The models enable estimation of extinction probabilities for different subpopulations by utilising data on the: 1) spatial distribution of sea lion foraging effort (based on satellite tracking studies), 2) relationship between rates of bycatch and the probability of interacting with sea lions, and 3) population viability analyses. The models can accommodate new data as it comes to hand and are designed to be flexible and easily modified by fishery and conservation managers, enabling the exploration and rapid assessment of different management scenarios.