Determining the effectiveness of a management system to enable fisheries to harvest sustainably is a key challenge. To fully assess the likelihood that a fishery management system will not achieve its sustainability objectives, the assessment needs to include the whole pathway that leads to the consequences for management objectives. A crucial aspect of the pathway is the inclusion of management controls. Effectiveness of these management controls determines whether the effects of human pressures on ecological components and their impacts are reduced to a level that will not impede management achieving their objectives. Ecological risk assessments do not provide sufficient information to make decisions about what to change specifically in a management system to ensure a fishery is sustainably managed. Bowtie analysis (BTA) is a method that logically connects the relationships between management objectives, management controls, threats, potential impacts of threats on the fishery resource and the consequences of those impacts on achieving the management objectives. The combination of bowtie analysis and ecological risk assessment enables managers, scientists and stakeholders to evaluate different management controls and research options in response to risk factors and track the effectiveness of the management system. We applied a three-step method of bowtie analysis stage 1, quantitative ecological risk assessment and bowtie analysis stage 2 to evaluate fisheries management and science. We demonstrate these steps using a case study of a commercially fished species in New South Wales, Australia.