Stakeholder knowledge was collected through questionnaires and cognitive maps and used to summarize biological, environmental, technical, management, and socio-economic factors for several deep-water fisheries, identifying regional management issues and solutions. The questionnaires and cognitive maps revealed different technical, environmental, and management concerns in these fisheries. Dissatisfaction with management was more at an implementation than a conceptual level, because the existing management measures were mostly considered fit for purpose. Further, catch-and-effort data provided by the fishing industry were used to calculate standardized landings per unit effort. The results suggested different trends over time for three deep-water stocks exploited by the same fleet. The examples demonstrate how stakeholder involvement and use of qualitative knowledge and quantitative data might improve the management process and stock assessments when data are limited.