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Conservation planning in South Africa has traditionally focussed on terrestrial ecosystems however more attention has recently been placed on planning for aquatic biodiversity. This shift has required that new data and methods be developed to model biodiversity pattern and process for freshwater ecosystems and translate them into a GIS-compatible format. A GIS is used at almost every stage of the conservation planning process but its success is dependent on the participation of stakeholder groups. A careful balance needs to be maintained between the stakeholders who provide data and expert knowledge and the GIS operator who creates and communicates information. As the stakeholders determine the accuracy and applicability of the final product, it is important to build and maintain networks between multi-disciplinary groups and keep the technical aspects of GIS as simple and transparent as possible. The aim of this paper is to examine how GIS has been used to develop data layers from field collections and expert knowledge and provide management options to decision makers. Lessons learnt from the conservation planning process show the importance of GIS as a tool for creating and communicating information and building networks between stakeholder groups.