Riparian habitat quality has a significant influence on the water quality of rivers, primary resources for urban and agricultural use. River water quality deteriorates where normal ecological functioning is disrupted by harmful impacts from nearby land-use types. Important rivers are typically managed and protected by government-led conservation programs. These programs often lack a key tool for efficient conservation management, habitat quality mapping. The Berg River, an important water source in South Africa, was used as a case-study to assess how habitat quality mapping could broaden the current scope of river conservation programs. The river faces threats from nearby urban settlements, industrial areas, mining, encroachment, and agricultural practices. The aim of this study was to develop habitat quality and habitat degradation maps for a section of the Berg River to assess the value that mapping holds for conservation managers and spatial planners. InVEST modelling software and ArcGIS was used to produce these habitat quality maps based on land-use/land-cover and threat impact data. The resulting maps showed several specific locations of heavily threatened and degraded riparian habitat that had not specifically been included in current government conservation management or spatial planning. Habitat quality mapping is an important tool that conservation managers and spatial planners can use to successfully address habitat degradation and protection while facing resource limitations, such as lack of funding. Oversight of degraded riparian habitats will lead to further decreases in river water quality, adversely affecting human welfare and local economies.