Topographic complexity is a fundamental structural property of benthic marine ecosystems that exists across all scales and affects a multitude of processes. Coral reefs are a prime example, for which this complexity has been found to impact water flow, species diversity, nutrient uptake, and wave-energy dissipation, among other properties. Despite its importance, only limited assessments are available regarding the distribution or range of topographic complexity within or between benthic communities. Here, we show substantial variability in topographic complexity over the entire inner-shelf seascape of a tropical island. Roughness, estimated in terms of fractal dimension, served as a proxy for topographic complexity, and was computed for linear transects (D_T), as well as the benthic surface (D_S). Spatial variability in both D_T and D_S was correlated with the known distribution of benthic cover types in the seascape. Transect roughness values ranged from 1.0 to 1.7, with features along the shelf edge being markedly anisotropic with an along-shore bias, whereas regions with high scleractinian coral cover were nearly isotropic and exhibited minimal directional bias. Surface-roughness values ranged from 2.0 in predominantly hardbottom areas with low coral cover to 2.5 in areas with high coral cover. Quantifying roughness across the substrates and biological communities for an entire seascape provides a synoptic view of its spatial variability at scales appropriate for numerous research efforts, including ecosystem studies, parameterizing hydrodynamic models, and designing monitoring programs.