A qualitative model was developed in Garp3 to capture and formalise knowledge about river rehabilitation and the management of an Atlantic salmon population. The model integrates information about the ecology of the salmon life cycle, the environmental factors that may limit the survival of key life stages and links with human activities such as agriculture, habitat rehabilitation and fishing. The overall aim of the model was to explore the effects of rehabilitation in the context of a complete life cycle scenario. The scenarios and simulations produced were able to explore these processes in the context of a complete life cycle, but at this scale the simulations were time consuming. Therefore, in addition to these scenarios a series of smaller demonstrator scenarios were developed that succinctly explored individual concepts within the system.