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The interaction of coral reefs, both chemically and physically, with the surrounding seawater is governed, at the smallest scales, by turbulence. Here, we review recent progress in understanding turbulence in the unique setting of coral reefs-how it influences flow and the exchange of mass and momentum both above and within the complex geometry of coral reef canopies. Flow above reefs diverges from canonical rough boundary layers due to their large and highly heterogeneous roughness and the influence of surface waves. Within coral canopies, turbulence is dominated by large coherent structures that transport momentum both into and away from the canopy, but it is also generated at smaller scales as flow is forced to move around branches or blades, creating wakes. Future work interpreting reef-related observations or numerical models should carefully consider the influence that spatial variation has on momentum and scalar flux.

We examine temporal variability of thermally driven baroclinic cross-shore exchange in the context of a tropical fringing reef system focusing on the role of tidally driven alongshore flow. Ensemble diurnal phase averaging of cross-shore flow at the Kilo Nalu Observatory (KNO) in Oahu, Hawaii, shows a robust diurnal signal associated with an unsteady buoyancy/diffusive dynamic balance, although significant variability is observed at subdiurnal time scales. In particular, persistent fortnightly variability in the cross-shore diurnal flow pattern is consistent with modulation by the semidiurnal alongshore tidal flow. The alongshore flow plays a direct role in the cross-shore exchange momentum balance via Coriolis acceleration but also affects the cross-shore circulation indirectly via its influence on vertical turbulent diffusion. An idealized linear theoretical model for thermally driven cross-shore flow is formulated using the long-term time-averaged diurnal dynamic balance at KNO as a baseline. The model is driven at leading order by the surface heat flux, with contributions from the alongshore flow and cross-shore wind appearing as linear perturbations. Superposition of the idealized solutions for Coriolis and time-varying eddy viscosity perturbations are able to reproduce key aspects of the fortnightly variability. Modifying the model to consider a more realistic alongshore flow and considering effects of nightly convection lead to further improvements in comparisons with KNO observations. The ability of the theoretical approach to reproduce the fortnightly patterns indicates that semidiurnal variations in the alongshore flow are effective in modulating the cross-shore flow via Coriolis and vertical turbulent transport mechanisms.

We investigate the fidelity of the Delta Simulation Model-2 (DSM2), a one-dimensional branched network hydrodynamics solver, which is used to model water quality and ecology in the Sacramento–San Joaquin Delta estuary. We find that while DSM2 reproduces the total flows well, it does not accurately represent the harmonic components of the tides and tidal modulation of subtidal flow. The inaccurate representation of tidal dynamics affects prediction of subtidal flows, flow splits at key junctions, and salinity. These deviations are the result of coarse spatial and temporal representation of tides as well as unrepresented estuarine physical processes. We propose and evaluate two types of schemes intended to improve fidelity: modifying the model domain and specifying fine grid and boundary conditions, and incorporating and parameterizing more complex physical processes into the 1-D model. We also develop a comprehensive protocol to evaluate the model in which we assess the fidelity of model results. In this protocol, we also include a decomposition of the model error into a systematic component because of model representation, and an unsystematic component, which includes errors from both unmodeled physical processes and data precision. Our analysis reveals that these recommendations would be effective provided they can be incorporated with model recalibration. Both our proposed schemes and the model evaluation process will be useful in analyzing models of networked surface water systems such as the Delta in which the distribution of observations is spatially inhomogeneous.

This paper, part of the collection of research comprising the State of Bay–Delta Science 2016, describes advances during the past decade in understanding flow dynamics and how water-quality constituents move within California’s Sacramento–San Joaquin River Delta (Delta). Water-quality constituents include salinity, heat, oxygen, nutrients, contaminants, organic particles, and inorganic particles. These constituents are affected by water diversions and other human manipulations of flow, and they greatly affect the quantity and quality of benthic, pelagic, and intertidal habitat in the Delta. The Pacific Ocean, the Central Valley watershed, human intervention, the atmosphere, and internal biogeochemical processes are all drivers of flow and transport in the Delta. These drivers provide a conceptual framework for presenting recent findings. The tremendous expansion of acoustic and optical instruments deployed in the Delta over the past decade has greatly improved our understanding of how tidal variability affects flow and transport. Sediment is increasingly viewed as a diminishing resource needed to sustain pelagic habitat and tidal marsh, especially as sea level rises. Connections among the watershed, Delta, and San Francisco Bay that have been quantified recently highlight that a landscape view of this system is needed, rather than consideration of each region in isolation. We discuss interactions of multiple drivers and information gaps.

Over the past 15 years, the development and application of multi-dimensional hydrodynamic models in San Francisco Bay and the Sacramento–San Joaquin Delta has transformed our ability to analyze and understand the underlying physics of the system. Initial applications of three-dimensional models focused primarily on salt intrusion, and provided a valuable resource for investigating how sea level rise and levee failures in the Delta could influence water quality in the Delta under future conditions. However, multi-dimensional models have also provided significant insights into some of the fundamental biological relationships that have shaped our thinking about the system by exploring the relationship among X2, flow, fish abundance, and the low salinity zone. Through the coupling of multi-dimensional models with wind wave and sediment transport models, it has been possible to move beyond salinity to understand how large-scale changes to the system are likely to affect sediment dynamics, and to assess the potential effects on species that rely on turbidity for habitat. Lastly, the coupling of multi-dimensional hydrodynamic models with particle tracking models has led to advances in our thinking about residence time, the retention of food organisms in the estuary, the effect of south Delta exports on larval entrainment, and the pathways and behaviors of salmonids that travel through the Delta. This paper provides an overview of these recent advances and how they have increased our understanding of the distribution and movement of fish and food organisms. The applications presented serve as a guide to the current state of the science of Delta modeling and provide examples of how we can use multi-dimensional models to predict how future Delta conditions will affect both fish and water supply.

Outflow from the Sacramento–San Joaquin Delta is a key parameter used in the management of the San Francisco Bay–Delta system. At present we can estimate this by assuming a steady state balance of inflows and outflows (Dayflow) or by direct measurement. In this paper, I explore differences between observed sub-tidal variations in measured outflow and Dayflow values using water level and flow data taken during the summer of 2015 and an analytical framework based on the sub-tidally filtered St. Vénant equations. This analysis shows that flows associated with sub-tidal water level variations in the Delta explain most of the difference between the two flow measures. These variations largely result from low-frequency variations in sea level in the coastal ocean and to wind stresses acting on Suisun Bay, with spring–neap variations in tides playing a lesser role. Overall, a comparison of Dayflow and the direct flow measurement for water years 2008 to 2014 shows that the two flow measures are in good agreement, although the root mean square difference between the two values (ca. 5,000 cfs) is comparable to—or larger than—typical low flow values of Dayflow.

Residual (subtidal) circulation profiles in estuaries with a large tidal amplitude-to-depth ratio often are quite complex and do not resemble the traditional estuarine gravitational circulation profile. This paper describes how a depth-normalized s-coordinate system allows for a more physical interpretation of residual circulation profiles than does a fixed vertical coordinate system in an estuary with a tidal amplitude comparable to the mean depth. Depth-normalized coordinates permit the approximation of Lagrangian residuals, performance of empirical orthogonal function (EOF) analysis, estimation of terms in the along-stream momentum equations throughout depth, and computation of a tidally averaged momentum balance. The residual mass transport velocity has an enhanced two-layer exchange flow relative to an Eulerian mean because of the Stokes wave transport velocity directed upstream at all depths. While the observed s-coordinate profiles resemble gravitational circulation, and pressure and friction are the dominant terms in the tidally varying and tidally averaged momentum equations, the two-layer shear velocity from an EOF analysis does not correlate with the along-stream density gradient. To directly compare to theoretical profiles, an extension of a pressure-friction balance in s coordinates is solved. While the barotropic riverine residual matches theory, the mean longitudinal density gradient and mean vertical mixing cannot explain the magnitude of the observed two-layer shear residual. In addition, residual shear circulation in this system is strongly driven by asymmetries during the tidal cycle, particularly straining and advection of the salinity field, creating intratidal variation in stratification, vertical mixing, and shear. © 2014 American Meteorological Society.

In branching channel networks, such as in the Sacramento–San Joaquin River Delta, junction flow dynamics contribute to dispersion of ecologically important entities such as fish, pollutants, nutrients, salt, sediment, and phytoplankton. Flow transport through a junction largely arises from velocity phasing in the form of divergent flow between junction channels for a portion of the tidal cycle. Field observations in the Georgiana Slough junction, which is composed of the North and South Mokelumne rivers, Georgiana Slough, and the Mokelumne River, show that flow phasing differences between these rivers arise from operational, riverine, and tidal forcing. A combination of Acoustic Doppler Current Profile (ADCP) boat transecting and moored ADCPs over a spring–neap tidal cycle (May to  June 2012) monitored the variability of spatial and temporal velocity, respectively. Two complementary drifter studies enabled assessment of local transport through the junction to identify small-scale intrajunction dynamics. We supplemented field results with numerical simulations using the SUNTANS model to demonstrate the importance of phasing offsets for junction transport and dispersion. Different phasing of inflows to the junction resulted in scalar patchiness that is characteristic of MacVean and Stacey’s (2011) advective tidal trapping. Furthermore, we observed small-scale junction flow features including a recirculation zone and shear layer, which play an important role in intra-junction mixing over time scales shorter than the tidal cycle (i.e., super-tidal time scales). The study period spanned open- and closed-gate operations at the Delta Cross Channel. Synthesis of field observations and modeling efforts suggest that management operations related to the Delta Cross Channel can strongly affect transport in the Delta by modifying the relative contributions of tidal and riverine flows, thereby changing the junction flow phasing.

Results are presented from an observational study of stratified, turbulent flow in the bottom boundary layer on the outer southeast Florida shelf. Measurements of momentum and heat fluxes were made using an array of acoustic Doppler velocimeters and fast-response temperature sensors in the bottom 3 m over a rough reef slope. Direct estimates of flux Richardson number R f confirm previous laboratory, numerical, and observational work, which find mixing efficiency not to be a constant but rather to vary with Fr t, Re b, and Ri g. These results depart from previous observations in that the highest levels of mixing efficiency occur for Fr t, 1, suggesting that efficient mixing can also happen in regions of buoyancy-controlled turbulence. Generally, the authors find that turbulence in the reef bottom boundary layer is highly variable in time and modified by nearbed flow, shear, and stratification driven by shoaling internal waves. © 2011 American Meteorological Society.

A one-dimensional numerical model that simulates the effects of whitecapping waves was used to investigate the importance of whitecapping waves to vertical mixing at a 3-meter-deep site in Franks Tract in the Sacramento-San Joaquin Delta over an 11-day period. Locally-generated waves of mean period approximately 2 s were generated under strong wind conditions; significant wave heights ranged from 0 to 0.3 m. A surface turbulent kinetic energy flux was used to model whitecapping waves during periods when wind speeds > 5 m s-1 (62% of observations). The surface was modeled as a wind stress log-layer for the remaining 38% of the observations. The model results demonstrated that under moderate wind conditions (5–8 m s-1 at 10 m above water level), and hence moderate wave heights, whitecapping waves provided the dominant source of turbulent kinetic energy to only the top 10% of the water column. Under stronger wind (> 8 m s-1), and hence larger wave conditions, whitecapping waves provided the dominant source of turbulent kinetic energy over a larger portion of the water column; however, this region extended to the bottom half of the water column for only 7% of the observation period. The model results indicated that phytoplankton concentrations close to the bed were unlikely to be affected by the whitecapping of waves, and that the formation of concentration boundary layers due to benthic grazing was unlikely to be disrupted by whitecapping waves. Furthermore, vertical mixing of suspended sediment was unlikely to be affected by whitecapping waves under the conditions experienced during the 11-day experiment. Instead, the bed stress provided by tidal currents was the dominant source of turbulent kinetic energy over the bottom half of the water column for the majority of the 11-day period.

Kelp forests are essential ecosystems in coastal regions around the world. They have large effects on flow structure, biogeochemical processes, and ecological dynamics. However, studies have yet to simulate these ecosystems in either regional ocean or global climate models. Here we describe and validate a model that simulates kelp forests in the water column for the ocean component of the Coupled Ocean-Atmosphere-Wave-Sediment-Transport model (COAWST V3.3) using a simple yet efficient linear regression approach to simulate kelp canopies. An in-situ dataset of 2-1/2 years, with and without kelp forest coverage around Isla Natividad (Baja CA, MX), allowed model validation for the main tidal constituents. We tested different vegetation drag coefficients and compared simulations with our canopy model against the standard vegetation module in COAWST. Results show that while both models simulate the velocities observed in the in situ dataset reasonably well, our model better represents turbulence kinetic energy through the water column as observed in laboratory experiments. This new kelp model can be helpful in ecology, physics, and biogeochemistry studies. [ABSTRACT FROM AUTHOR]

Kelp forests are essential ecosystems in coastal regions around the world. They have large effects on flow structure, biogeochemical processes, and ecological dynamics. However, studies have yet to simulate these ecosystems in either regional ocean or global climate models. Here we describe and validate a model that simulates kelp forests in the water column for the ocean component of the Coupled Ocean-Atmosphere-Wave-Sediment-Transport model (COAWST V3.3) using a simple yet efficient linear regression approach to simulate kelp canopies. An in-situ dataset of 2-1/2 years, with and without kelp forest coverage around Isla Natividad (Baja CA, MX), allowed model validation for the main tidal constituents. We tested different vegetation drag coefficients and compared simulations with our canopy model against the standard vegetation module in COAWST. Results show that while both models simulate the velocities observed in the in situ dataset reasonably well, our model better represents turbulence kinetic energy through the water column as observed in laboratory experiments. This new kelp model can be helpful in ecology, physics, and biogeochemistry studies. [ABSTRACT FROM AUTHOR]