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In the coastal ocean, interactions of waves and currents with large roughness elements, similar in size to wave orbital excursions, generate drag and dissipate energy. These boundary layer dynamics differ significantly from well-studied small-scale roughness. To address this problem, we derived spatially and phase-averaged momentum equations for combined wave–current flows over rough bottoms, including the canopy layer containing obstacles. These equations were decomposed into steady and oscillatory parts to investigate the effects of waves on currents, and currents on waves. We applied this framework to analyse large-eddy simulations of combined oscillatory and steady flows over hemisphere arrays (diameter $D$ ), in which current ( $U_c$ ), wave velocity ( $U_w$ ) and period ( $T$ ) were varied. In the steady momentum budget, waves increase drag on the current, and this is balanced by the total stress at the canopy top. Dispersive stresses from oscillatory flow around obstacles are increasingly important as $U_w/U_c$ increases. In the oscillatory momentum budget, acceleration in the canopy is balanced by pressure gradient, added-mass and form drag forces; stress gradients are small compared to other terms. Form drag is increasingly important as the Keulegan–Carpenter number $KC=U_wT/D$ and $U_c/U_w$ increase. Decomposing the drag term illustrates that a quadratic relationship predicts the observed dependences of steady and oscillatory drag on $U_c/U_w$ and $KC$ . For large roughness elements, bottom friction is well represented by a friction factor ( $f_w$ ) defined using combined wave and current velocities in the canopy layer, which is proportional to drag coefficient and frontal area per unit plan area, and increases with $KC$ and $U_c/U_w$ . 

In shallow water systems like coral reefs, bottom friction is an important term in the momentum balance. Parameterizations of bottom friction require a representation of canopy geometry, which can be conceptualized as an array of discrete obstacles or a continuous surface. Here, we assess the implications of using obstacle‐ and surface‐based representations to estimate geometric properties needed to parameterize drag. We collected high‐resolution reef topography data using a scanning multibeam sonar that resolved individual coral colonies within a set of 100‐m²reef patches primarily composed of moundingPoritescorals. The topography measurements yielded 1‐cm resolution continuous surfaces consisting of a single elevation value for each position in a regular horizontal grid. These surfaces were analyzed by (1) defining discrete obstacles and quantifying their properties (dimensions, shapes), and (2) computing properties of the elevation field (root mean square (rms) elevations, rms slopes, spectra). We then computed the roughness density (i.e., frontal area per unit plan area) using both analysis approaches. The obstacle and surface‐based estimates of roughness density did not agree, largely because small‐scale topographic variations contributed significantly to total frontal area. These results challenge the common conceptualization of shallow‐water canopies as obstacle arrays, which may not capture significant contributions of high‐wavenumber roughness to total frontal area. In contrast, the full range of roughness length scales present in natural reefs is captured by the continuous surface representation. Parameterizations of bottom friction over reef topography could potentially be improved by representing the contributions of all length scales to total frontal area and drag.