A common issue faced by fisheries and marine protected species managers is how to estimate the potential impacts of bycatch and identify appropriate options for mitigation, in the absence of quantitative data. This problem formed the basis to a risk-assessment study aimed at quantifying the risks to Australian sea lion ( Neophoca cinerea) and New Zealand fur seal ( Arctocephalus forsteri) populations from bycatch in a trap (rock lobster) and demersal gillnet fishery off South Australia. The approach was to: (1) estimate the spatial distribution of foraging effort for different sex and age classes within each species; (2) compare these with the spatial distribution of fishing effort in order to develop spatial estimates of seal-fishery interaction probabilities; (3) undertake population viability analyses to identify the levels of bycatch that would place subpopulations of each species into different risk categories; and (4) examine different bycatch scenarios and identify subpopulations, regions and marine fishing areas with the greatest bycatch risk. Results suggest that the risk of subpopulation extinction, even from low levels of bycatch, was high for sea lions, but very low for fur seals and that the two fisheries lend themselves to different mitigation approaches: gear modification in the lobster fishery, and spatial management of fishing effort in the demersal gillnet fishery.