Coral reefs are highly dynamic and productive marine ecosystems, providing habitat and refuge for an enormous number of species including fish, invertebrates and algae. With increased anthropogenic pressures and global climate change, many coral reefs are rapidly declining. Currently, there is limited knowledge on condition and community assemblage composition of shallow fringing coral reefs along the south-eastern coast of Queensland, Australia. With increased demand to determine existence of coastal fringing reefs by National Regional Management groups, a rapid cost effective method to determine reef composition and condition was required. The aim of this study was to determine the benthic structure and extent of two small coastal fringing reefs (Hummock Hill Reef and Stringers Reef) along the Southern Great Barrier Reef. Reef substrate assessments were carried out using a rapid assessment technique and a Point Intercept Method (PIM). The data were analysed and classified using a Geographic Information System (GIS). Percent substrate cover was calculated using a visual basic image analysis program. The Point intercept method showed higher accuracy over the rapid assessment technique (up to 15–40% difference) and was thus deemed a more suitable classification tool for reefs with high structural complexity and heterogeneity. This study focused on piloting a rapid, cost effective Point Intercept Technique using random point count methodology to document coral benthic habitat and extent over a commonly used rapid assessment method as a tool for reef coastal management and conservation. The two techniques were compared and substrate classification success, limitations and errors were discussed.