The Great Barrier Reef (GBR) is assumed to be a tectonically stable area, but recent studies show that neotectonic activity could have affected the geomorphology and evolution of the coral reefs. We used bathymetry, free-air gravity and 2D seismic data to test the hypothesis that neotectonic (i.e. geologically recent or currently active) faults have affected the morphology and major aspects of reefs' growth in the northernmost zone of the GBR, 13.5 degrees S-10.5 degrees S. Bathymetry data show that elongated reef platforms, oriented WNW-ESE, are systematically deflected at their ends or, in some cases, offset through their bodies, along interpreted structural lineaments. Submarine stream channels, running mostly in WNW-ESE orientations, have deepened their courses within the areas occupied by elongated platforms. The deflection or offset of the coral reefs is interpreted to result from movement on neotectonic faults based on the following lines of evidence: (1) fault lineaments based on reef platform morphology are almost parallel to those interpreted from free-air gravity data, consistent with deep-seated faults; (2) offsets along the deflected zones of reef platforms are oriented sub-parallel to interpreted fault lineaments, consistent with those faults having deformed reef morphology since reef initiation; (3) some inferred fault positions correspond to faults interpreted from limited 2D seismic reflection data; (4) fluvial incision of the continental shelf between elongated reefs is consistent with neotectonic fault activity; and (5) M > 4 earthquakes have been recorded adjacent to some interpreted lineaments. We propose that the GBR has been affected by localised active tectonism in different ways. Small, localised faults active in the late Pleistocene displaced and deflected coral reefs laterally in the northernmost zone of the GBR. In the central zone of the GBR larger (NNE-SSW trending) bounding faults controlled regional subsidence, thus affecting accommodation and broader reef growth patterns. Our results suggest that recently active faults in the GBR have had, and may continue to have, important ramifications for the developmental history of the reef province. These findings are significant given that the assumption of tectonic stability underpins many interpretations of the potential effects of changing climate and sea level on reef growth.