Human activities related to land use and land development (e.g. intensification of dairy farming and irrigation) are key factors involved in the alteration, and destruction of aquatic and related ecosystems in rural regions. Restoration as a means to re-establish functions and related physical, chemical and biological characteristics of a degraded and disturbed system (Cairns, 1988), can have a considerable role in minimizing the effects of human activities on streams and downstream aquatic systems (Ministry for the Environment, 2000). Additionally, restoration can result in the enhancement of stream habitat and water quality. The aim of this research was to develop a GIS-based decision support system that facilitated and improved both stream-reach and onsite riparian restoration efforts. The support system had a further goal of prioritising sections and sites with respect to their suitability for restoration efforts specifically in the New Zealand context. Using two spatial scales in the analysis took into account the importance of scale for dealing with restoration issues. First, the stream-reach scale allowed a broader scaled strategic planning of restoration efforts; and second, the onsite scale analysis supported the restoration work at which scale the restoration ultimately occurs (Harris et al., 1997). The application of stage one of the GIS-based decision support system at the Temuka Catchment, and stage two at the Waihi River in the Temuka Catchment, demonstrated that this research successfully implemented an ecological restoration mapping challenge into a GIS system. By testing different criteria weights in four scenarios, at stage one of the decision support system, a range of degradation was found in the total riparian area. Concentrated efforts can then be directed to those areas consistently analysed as low or not degraded.