Coral and sandstone reefs cover a significant part of Sri Lanka’s continental shelf and contain in comparison unique reef structures. Despite this, reefs in this region of the northern Indian Ocean have received little research attention. In an attempt to better understand these ecosystems and their innate character, this study describes the variety of reef types and habitats that are found in this area. The study concentrated on four major reef areas: the Bar Reef Marine Sanctuary (BRMS), Kandakuliya Reefs, Talawila Reef, and Mampuri Reef. These reefs showed apparent differences in habitat structure in terms of the proportion coral cover, coral species composition and structural complexity. Two reef types were present within the continental shelf of BRMS: coral and sandstone patch-reefs. Acropora was the most dominant coral genera however in total 118 madreporarian species and 50 coral genera were recorded in the sanctuary. Distinct habitats were identified within reef types including shallow reef flat, shallow patch reef, deep reef flat and Porites dome habitats for the coral-reef patches while the sandstone-reef patches were divided into structured and flat sandstone reef habitats. Kandakuliya Reef south of BRMS was by large dominated by coral rubble. Talawila Reef and Mampuri Reef showed unique structures with the former being dominated by massive corals and the latter mainly containing sandstone structures. In addition to factors such as bio-erosion, sedimentation, hydrodynamics, and recruitment or colonisation processes, some reefs were clearly under significant direct human impact which appeared to play a dominant role in habitat structuring. However, type and degree of human disturbance varied among the reefs. Habitat alteration at Kandakuliya Reef was the result of intense fishing using destructive fishing methods. Talawila Reef and Mampuri Reef was also influenced by fishing activities though reef structure seemed less affected.