Sarah N. Giddings

High-resolution simulations of a macrotidal estuary using SUNTANS

The parallel, finite-volume, unstructured-grid SUNTANS model has been employed to study the interaction of the tides with complex bathymetry in the macrotidal Snohomish River estuary. The unstructured grid resolves the large-scale, O(10 km) tidal dynamics of the estuary while employing 8 m grid-resolution at a specific region of interest in the vicinity of a confluence of two channels and extensive intertidal mudflats to understand detailed local intratidal flow processes. After calibrating tidal forcing parameters to enforce a match between free surface and depth-averaged velocities at several locations throughout the domain, we analyze the complex dynamics of the confluence and show that the exposure of the intertidal mudflats during low tide induces a complex flow reversal. When coupled with the longitudinal salinity gradient, this flow reversal results in a highly variable salinity field, which has profound implications for local mixing, stratification and the occurrence of fine-scale flow structures. This complex flow is then used as a testbed from which to describe several challenges associated with high resolution modeling of macrotidal estuaries, including specification of high resolution bathymetry, specification of the bottom stress, computation of the nonhydrostatic pressure, accurate advection of momentum, and the influence of the freshwater inflow. The results indicate that with high resolution comes the added difficulty of requiring more accurate specification of boundary conditions. In particular, the bottom bathymetry plays the most important role in achieving accurate predictions when high resolution is employed. 2008 Elsevier Ltd. All rights reserved.

Hindcasts of potential harmful algal bloom transport pathways on the Pacific Northwest coast

Harmful algal blooms (HABs) pose a significant threat to human and marine organism health, and negatively impact coastal economies around the world. An improved understanding of HAB formation and transport is required to improve forecasting skill. A realistic numerical simulation of the US Pacific Northwest region is used to investigate transport pathways from known HAB formation hot spots, specifically for Pseudo-nitzschia (Pn), to the coast. We show that transport pathways are seasonal, with transport to the Washington (WA) coast from a northern source (the Juan de Fuca Eddy) during the summer/fall upwelling season and from a southern source (Heceta Bank) during the winter/early spring due to the predominant wind-driven currents. Interannual variability in transport from the northern source is related to the degree of wind intermittency with more transport during years with more frequent relaxation/downwelling events. The Columbia River plume acts to mitigate transport to the coast as the plume front blocks onshore transport. The plumes influence on alongshore transport is variable although critical in aiding transport from the southern source to the WA coast via plume entrainment. Overall transport from our simulations captures most observed Pn HAB beach events from 2004 to 2007 (characterized by Pseudo-nitzschia cell abundance); however, numerous false positives occur. We show that incorporating phytoplankton biomass results from a coupled biogeochemical model reduces the number of false positives significantly and thus improves our Pn HAB predictions. Key Points Potential PNW HAB transport is seasonal, consistent with regional currents Transport is blocked by the Columbia River plume unless entrainment occurs A coupled hydrodynamic-biological model can predict PNW Pn HAB transport paths

Seasonal and interannual oxygen variability on the Washington and Oregon continental shelves

The coastal waters of the northern portion of the California Current System experience a seasonal decline in oxygen concentrations and hypoxia over the summer upwelling season that results in negative impacts on habitat for many organisms. Using a regional model extending from 43°N to 50°N, with an oxygen component developed in this study, drivers of seasonal and regional oxygen variability are identified. The model includes two pools of detritus, which was an essential addition in order to achieve good agreement with the observations. The model was validated using an extensive array of hydrographic and moored observations. The model captures the observed seasonal decline as well as spatial trends in bottom oxygen. Spatially, three regions of high respiration are identified as locations where hypoxia develops each modeled year. Two of the regions are previously identified recirculation regions. The third region is off of the Washington coast. Sediment oxygen demand causes the region on the Washington coast to be susceptible to hypoxia and is correlated to the broad area of shallow shelf (<60 m) in the region. Respiration and circulation-driven divergence contribute similar (60, 40%, respectively) amounts to the integrated oxygen budget on the Washington coast while respiration dominates the Oregon coast. Divergence, or circulation, contributes to the oxygen dynamics on the shelf in two ways: first, through the generation of retention features, and second, by determining variability.

Estuary-enhanced upwelling of marine nutrients fuels coastal productivity in the U.S. Pacific Northwest

© 2014. American Geophysical Union. All Rights Reserved. The Pacific Northwest (PNW) shelf is the most biologically productive region in the California Current System. A coupled physical-biogeochemical model is used to investigate the influence of freshwater inputs on the productivity of PNW shelf waters using realistic hindcasts and model experiments that omit outflow from the Columbia River and Strait of Juan de Fuca (outlet for the Salish Sea estuary). Outflow from the Strait represents a critical source of nitrogen to the PNW shelf-accounting for almost half of the primary productivity on the Vancouver Island shelf, a third of productivity on the Washington shelf, and a fifth of productivity on the Oregon shelf during the upwelling season. The Columbia River has regional effects on the redistribution of phytoplankton, but does not affect PNW productivity as strongly as does the Salish Sea. A regional nutrient budget shows that nitrogen exiting the Strait is almost entirely (98%) of ocean-origin - upwelled into the Strait at depth, mixed into surface waters by tidal mixing, and returned to the coastal ocean. From the standpoint of nitrogen availability in the coastal euphotic zone, the estuarine circulation driven by freshwater inputs to the Salish Sea is more important than the supply of terrigenous nitrogen by rivers. Nitrogen-rich surface waters exiting the Strait follow two primary pathways - to the northwest in the Vancouver Island Coastal Current and southward toward the Washington and Oregon shelves. Nitrogen flux from the Juan de Fuca Strait and Eddy Region to these shelves is comparable to flux from local wind-driven upwelling.

Frontogenesis and Frontal Progression of a Trapping-Generated Estuarine Convergence Front and Its Influence on Mixing and Stratification

Estuarine fronts are well known to influence transport of waterborne constituents such as phytoplankton and sediment, yet due to their ephemeral nature, capturing the physical driving mechanisms and their influence on stratification and mixing is difficult. We investigate a repetitive estuarine frontal feature in the Snohomish River Estuary that results from complex bathymetric shoal/channel interactions. In particular, we highlight a trapping mechanism by which mid-density water trapped over intertidal mudflats converges with dense water in the main channel forming a sharp front. The frontal density interface is maintained via convergent transverse circulation driven by the competition of lateral baroclinic and centrifugal forcing. The frontal presence and propagation give rise to spatial and temporal variations in stratification and vertical mixing. Importantly, this front leads to enhanced stratification and suppressed vertical mixing at the end of the large flood tide, in contrast to what is found in many estuarine systems. The observed mechanism fits within the broader context of frontogenesis mechanisms in which varying bathymetry drives lateral convergence and baroclinic forcing. We expect similar trapping-generated fronts may occur in a wide variety of estuaries with shoal/channel morphology and/or braided channels and will similarly influence stratification, mixing, and transport.

Using Depth-Normalized Coordinates to Examine Mass Transport Residual Circulation in Estuaries with Large Tidal Amplitude Relative to the Mean Depth

AbstractResidual (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 σ-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 σ-coordinate profiles resemble gravitational circulation, and pressure and fricti...

The Mechanical Energy Budget of a Regional Ocean Model

AbstractA method is presented for calculating a complete, numerically closed, mechanical energy budget in a realistic simulation of circulation in a coastal–estuarine domain. The budget is formulated in terms of the “local” available potential energy (APE; Holliday and McIntyre 1981). The APE may be split up into two parts based on whether a water parcel has been displaced up or down relative to its rest depth. This decomposition clearly shows the different APE signatures of coastal upwelling (particles displaced up by wind) and the estuary (particles displaced down by mixing). Because the definition of APE is local in almost the same sense that kinetic energy is, this study may form meaningful integrals of reservoir and budget terms even over regions that have open boundaries. However, the choice of volume to use for calculation of the rest state is not unique and may influence the results. Complete volume-integrated energy budgets over shelf and estuary volumes in a realistic model of the northeast Paci...