Estuaries around the world are often degraded and subject to issues surrounding effective management and governance. Without substantial changes in the overall management of many catchments, there is a risk that estuarine health will further decline, causing serious social and economic impacts. The Peel region is one of Australia's fastest growing residential areas and the social and economic wellbeing of the local community is tied to the health of the Peel-Harvey estuary. This estuary is the largest in south Western Australia and has for decades incurred considerable anthropogenic impacts. This study uses the Peel-Harvey estuary as a case study for the assessment of governance structures and ecosystem dynamics using qualitative models. Each model highlights drivers that impact the most important assets, water quality and general environmental quality. Potential management strategies are identified to tackle ineffective monitoring and regulation of impacts, overlapping responsibilities between different public infrastructure providers, and a lack of accountability. Incorporating 'ideal' management strategies into 'future' models clarified paths of governance and provided better delivery of outcomes. Strong environmental and nutrient management were integral to effective environmental governance, as was the need for whole-of-government environmental decisions to be made in the context of predicted longer-term benefits for all sectors, including the general community. The assessment of social-ecological structures, issues and potential management strategies using qualitative models identified mechanisms to achieve effective management and resulted in predictions of increased environmental quality, as well as increased social and economic values. © 2013 Elsevier Ltd.