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Abstract Most work on how estuarine dynamics impact dissolved oxygen (DO) distributions has focused on tides, but in shallow estuaries with large fetch or small tides, wind can be the primary mixing agent and also drives advection. To investigate how these processes affect DO distributions, an observational study was conducted in the shallow, microtidal Neuse Estuary. Salinity, DO, and velocity profiles were measured at multiple positions along and across the estuary over a 6‐month period. A one‐dimensional model (General Ocean Turbulence Model) provided additional insight into the response of salinity and DO to wind. Salinity and oxygen conservation equation terms were calculated from observations and simulations. Cross‐estuary wind drove lateral circulation and tilted the isohalines, reducing stratification; lateral advection and enhanced mixing reduced vertical gradients and increased the bottom DO. Down‐estuary wind tended to increase the exchange flow and stratification, but concurrently the surface wind‐mixed layer deepened over time. The balance of these processes determined if the water column became fully mixed or remained stratified, and the depth of the pycnocline and oxycline. An expression for steady state surface layer thickness was derived by considering the competition between the horizontal and vertical buoyancy flux, and the predictions agreed well with observations and simulations. Up‐estuary wind inhibited the exchange flow and the combination of advection and mixing homogenized the water column. While these patterns generally held for purely across‐ or along‐channel wind, the response was often more complex as the wind vector varied in orientation and with time. 

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 $$U_c/U_w$$ . 

Abstract 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.