Fisheries management is not only about managing the resource fish, but also includes managing the social system. Aquatic ecosystems and the social system are both complex and change continuously. It is important to address what types of uncertainty the combination of both systems, complex socio-ecological systems leads to, their consequences and how these should be dealt with. Successful or unsuccessful management outcomes are difficult to address whether or not they are due to management efforts or natural changes. In addition, uncertainties often lead to a short-term management, since lack of knowledge makes it difficult to act in a long-term perspective. This thesis conceptualizes how to address different types of uncertainty prevalent in fisheries management, with focus on natural process uncertainty, measurement and estimation uncertainty, decision and implementation uncertainty, and institutional and regime uncertainty.  This was done by analyzing how three theoretical approaches, namely co-management, adaptive management and adaptive co-management address these uncertainties. In order to highlight how different types of uncertainty have been dealt with in practice, a case study on the fishery management in Lake Vättern has been made. A comparison between the literature study and this thesis’ case study shows that hypothesis-testing, cooperation, communication and transparency are corresponding factors on how to deal with uncertainties in fisheries management and that institutional and regime uncertainty is inadequately addressed in Sweden.