The physical structure of coral reefs plays a critical role as a barrier to storm waves and tsunamis and as a habitat for living reef-building and reef-associated organisms. However, the mechanical properties of reef substrate (i. e. the non-living benthos) are largely unknown, despite the fact that substrate properties may ultimately determine where organisms can persist. We used a geo-mechanical technique to measure substrate material density and strength over a reef hydrodynamic gradient. Contrary to expectation, we found a weak relationship between substrate strength and wave-induced water flow: flow rates decline sharply at the reef crest, whereas substrate properties are relatively constant over much of the reef before declining by almost an order of magnitude at the reef back. These gradients generate a novel hump-shaped pattern in resistance to mechanical disturbances for live corals, where colonies closer to the back reef are prone to dislodgement because of poorly cemented substrate. Our results help explain an intermediate zone of higher taxonomic and morphological diversity bounded by lower diversity exposed reef crest and unstable reef back zones.