The historical approach of sector-specific, largely top-down management in favor of highly capitalized industry sectors has seemingly left southern Benguela fisheries management in a Gordian knot. The modern systems approach to management of human activities in the oceans forbids cutting through the knot, making it necessary to develop methodology for including a wide range of stakeholders and trading off multiple, conflicting objectives under high uncertainty. Recent research in an interdisciplinary group including researchers and students from the humanities, social and natural sciences has focused on soft predictability and structured decision making in social-ecological marine systems under global change. Using three management case studies from the southern Benguela, i.e. purse-seine fisheries, conservation of the Endangered African penguin and the commercial handline fishery system in the southern Cape, we review how modelling system dynamics with stakeholders, semi-quantitative methodology for the integration of a wide variety of indicators, social learning, communication around shared issues and dedicated trust building have supported softening of boundaries between stereotyped stakeholders, and are contributing to a shared knowledge base as well as to an extended toolkit for management. We highlight promising loops of the knot with a view of generating discussion on how these can be tackled strategically.