We assessed the independent effects of natural physical drivers in structuring coral reef benthic communities at a remote oceanic atoll in the central equatorial Pacific with minimal local human impacts. High-resolution bathymetric data combined with in situ oceanographic measurements and a nearshore hydrodynamic model revealed complex intra-atoll gradients in geomorphic complexity, wave forcing, currents, and temperature. For example, maximum wavedriven bed shear stress spatially varied on the forereef (15−20 m depth) by over 2 orders of magnitude, peaking in areas exposed to multiple wave regimes. Benthic community composition, quantified via towed-diver imagery collected in a complete circumnavigation of the atoll (~40 km), also exhibited considerable spatial heterogeneity. Benthic competitors showed distinct, non-linear threshold-type responses to variations in physical drivers. For example, at a wave-driven bed shear stress threshold of 18 N m−2, calcifying crustose coralline algae lost relative dominance and were replaced by non-calcifying fleshy turf algae. Hard coral communities also demonstrated considerable flexibility in response to physical drivers, with distinct shifts in the relative dominance of different growth morphologies along gradients of wave forcing, presumably as a means of local adaptation. Our results highlight (1) the importance of natural gradients in physical drivers in determining dominant benthic regimes on coral reefs (e.g. calcifying vs. fleshy), (2) that non-linear thresholds (or tipping points) exist between key benthic competitors in response to key physical drivers, and (3) that coral assemblages show inherent flexibility and can reorganize in response to physical drivers rather than exhibit wholesale changes in overall cover.