| Summary: | Includes bibliographical references (p. 125-140). === Freshwater ecosystems underpin the fabric of society and the environment, providing essential ecosystem services such as water and food, upon which all human beings depend. In order to secure these vital services requires the sustainable management of freshwater ecosystems. At present however, freshwater biodiversity is under severe threat from anthropogenic disturbances, and the situation is expected to worsen due to population growth and global change. Coupled with the threats to freshwater biota are the limited resources available to secure their protection. There is a need to therefore prioritise freshwater ecosystems in a comprehensive, adequate and representative manner to maximise the outcomes of conservation effort. The concept of systematic conservation planning was developed to address this challenge. It offers a suitable framework for achieving conservation goals in the face of other competing land uses. The principles of systematic conservation planning are being widely applied in terrestrial and marine ecosystems, but their application in freshwater ecosystems is still relatively limited. Freshwater ecosystems provide challenges to conservation planning that are unique from those of terrestrial and marine ecosystems, such as the longitudinal nature of river systems and the associated connectivity, and catchment divides that constrain some obligate species. As a result freshwater ecosystems require conservation planning tools and approaches that are specifically geared towards addressing these unique challenges. Progress has recently been achieved in addressing some of these challenges, but there are still other outstanding issues that have not been comprehensively addressed. The aim of this thesis was to develop new frameworks, and test approaches for the application of systematic conservation planning principles in the conservation of freshwater ecosystems in South Africa. The thesis addressed a range of issues along the systematic conservation planning continuum from biodiversity assessment to implementation. I first carried out a focused review of systematic conservation literature between 1987- 2006, to gauge the extent to which freshwater ecosystems have being integrated in conservation assessments. Most of the focus was found to be on terrestrial ecosystems with minimal incorporation of freshwater biodiversity. Wetlands for example, were in most cases incorporated into conservation assessments without taking their diversity into account. This was partly attributed to the difficulty of classifying wetlands. I therefore developed and tested a hierarchical GIS framework for automating wetland classification as a strategy for incorporating wetland biodiversity, functions and benefits into broad scale conservation planning.
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