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The feasibility of reducing nutrient pollution impacts by redirecting excess nutrient flux away from the photic zone is investigated. Alternate effluent discharge strategies to avoid or bypass the euphotic zone were tested under the hypothesis that in deep estuaries, depth of the surface exchange outflow layer may be greater than euphotic zone depth, providing opportunity for a fraction of the nutrient pollution to be exported out passively. We used the Salish Sea region in the Pacific Northwest as a test bed for this assessment. Euphotic zone depth in the Puget Sound basin of Salish Sea in U.S waters varies from 8 m to 25 m while the depth of outflow layer is approximately 60m. Sensitivity of biological response and water quality impact were quantified using an established biophysical model of the system, using exposure to low DO levels as the metric (< 2 mg/L hypoxia and < 5 mg/L impairment). Opportunity to reduce nutrient pollution impact was tested through outfall relocation strategies, applied to 99% of the anthropogenic loads currently delivered to the Puget Sound. The results show that relative to natural impairment levels, marine wastewater outfalls are responsible for 36% of increase, while loads from upstream watersheds that enter Puget Sound via river flows, are responsible for 70% of increase in impairment. Results were consistent with the hypothesis in that moving the outfalls to deeper waters resulted in reduced primary production. However, in some basins, the benefits of lower water column respiration were offset by reduced DO production and were accompanied by some loss in the strength of circulation. Puget Sound basin results indicate worsening of DO impairment hours (average +3.0%), while Whidbey Basin showed improvement in DO impairment hours (-6.8%) relative to existing conditions. The results indicate that presence of multiple sills and the associated reflux flows / circulation obstruct the export of nutrients out of the system. The efforts to relocate outfalls to achieve euphotic zone bypass and improve DO impairment were therefore not as effective as hypothesized.

This study used suspect and nontarget screening with high-resolution mass spectrometry to characterize the occurrence of contaminants of emerging concern (CECs) in the nearshore marine environment of Puget Sound (WA). In total, 87 non-polymeric CECs were identified; those confirmed with reference standards (45) included pharmaceuticals, herbicides, vehicle-related compounds, plasticizers, and flame retardants. Eight polyfluoroalkyl substances were detected; perfluorooctanesulfonic acid (PFOS) concentrations were as high as 72-140 ng/L at one location. Low levels of methamphetamine were detected in 41% of the samples. Transformation products of pesticides were tentatively identified, including two novel transformation products of tebuthiuron. While a hydrodynamic simulation, analytical results, and dilution calculations demonstrated the prevalence of wastewater effluent to nearshore marine environments, the identity and abundance of selected CECs revealed the additional contributions from stormwater and localized urban and industrial sources. For the confirmed CECs, risk quotients were calculated based on concentrations and predicted toxicities, and eight CECs had risk quotients1. Dilution in the marine estuarine environment lowered the risks of most wastewater-derived CECs, but dilution alone is insufficient to mitigate risks of localized inputs. These findings highlighted the necessity of suspect and nontarget screening and revealed the importance of localized contamination sources in urban marine environments.

Between the land and ocean, diverse coastal ecosystems transform, store, and transport material. Across these interfaces, the dynamic exchange of energy and matter is driven by hydrological and hydrodynamic processes such as river and groundwater discharge, tides, waves, and storms. These dynamics regulate ecosystem functions and Earth’s climate, yet global models lack representation of coastal processes and related feedbacks, impeding their predictions of coastal and global responses to change. Here, we assess existing coastal monitoring networks and regional models, existing challenges in these efforts, and recommend a path towards development of global models that more robustly reflect the coastal interface., Coastal systems are hotspots of ecological, geochemical and economic activity, yet their dynamics are not accurately represented in global models. In this Review, Ward and colleagues assess the current state of coastal science and recommend approaches for including the coastal interface in predictive models.

The restoration of eelgrass (Zostera marina L.) is a high priority in Puget Sound, Washington, United States. In 2011, the state set a restoration target to increase eelgrass area by 4,200 ha by 2020, a 20% increase over the 21,500 ha then present. In a region as large, dynamic and complex as Puget Sound, locating areas to restore eelgrass effectively and efficiently is challenging. To identify potential restoration sites we used simulation modeling, a geodatabase for spatial screening, and test planting. The simulation model of eelgrass biomass used time series of water properties (depth, temperature, and salinity) output from a regional hydrodynamic model and empirical water clarity data to indicate growth potential. The GIS-based analysis incorporated results from the simulation model, historical and current eelgrass area, substrate, stressors, and shoreline manager input into a geodatabase to screen sites for field reconnaissance. Finally, we planted eelgrass at test sites and monitored survival. We screened 2,630 sites and identified 6,292 ha of highly to very highly suitable conditions for eelgrass-ample area for meeting the 20% target. Test plantings indicated fine-scale data needs to improve predictive capability. We summarized the results of our analysis for the majority of the ~3,220 km of shoreline in Puget Sound on maps to support restoration site selection and planning. Our approach provides a process for identifying and testing potential restoration sites and highlights information needs and management actions to reduce stressors and increase eelgrass area to meet restoration objectives.

Although the Snohomish River estuary remains the second largest tidal wetland complex in Puget Sound, approximately 90% of pre-settlement habitat has been disconnected from tidal exchange. This estuary is currently the focus of the largest restoration effort in Puget Sound, with opportunity to restore tidal exchange to over 50% of pre-settlement levels. The Snohomish River also currently supports populations of all anadromous Pacific salmon species, including Endangered Species Act listed Chinook (Oncorhynchus tshawytscha), steelhead (O. mykiss), and bull trout (Salvelinus confluentus). The combination of extant anadromous Pacific salmon populations, large existing tidal wetland complexes, and large restoration potential make the Snohomish River estuary a great opportunity to benefit salmon population recovery and conservation efforts. To support restoration planning and effectiveness monitoring, we developed baseline characterizations of key physical attributes (salinity and temperature). Our results indicated that brackish (0.5–30 ppt) conditions extended farther upriver than previously described, with distributary channels downstream of the middle mainstem and lower Ebey Slough remaining brackish throughout most of the year. During extreme low flows ( 0.5 ppt) can at times intrude throughout the distributaries and up to river kilometer 15.9 above the first bifurcation. We also observed temperatures exceeding stress thresholds for juvenile salmonids throughout the estuary from July through September, a period that overlaps with juvenile rearing. This research is timely with several large restoration projects scheduled for construction by 2020, and these baseline characterizations can be used to evaluate restoration responses, as well as to inform project prioritization and monitoring.

The Salish Sea consisting of Puget Sound and Georgia Basin in U.S and Canadian waters has been the subject of several independent data collection and modeling studies. However, these interconnected basins and their hydrodynamic interactions have not received attention as a contiguous unit. The Strait of Juan de Fuca is the primary pathway through which Pacific Ocean water enters the Salish Sea but the role played by Johnstone Strait and the complex channels northeast of Vancouver Island, connecting the Salish Sea and the Pacific Ocean, on overall Salish Sea circulation has not been characterized. In this paper we present a modeling-based assessment of the two-layer circulation and transport through the multiple interconnected sub-basins within the Salish Sea including the effect of exchange via Johnstone Strait and Discovery Islands. The Salish Sea Model previously developed using the finite volume community ocean model (FVCOM) was expanded over the continental shelf for this assessment encircling Vancouver Island, including Discovery Islands, Johnstone Strait, Broughton Archipelago and the associated waterways. A computational technique was developed to allow summation of volume fluxes across arbitrary transects through unstructured finite volume cells. Tidally averaged volume fluxes were computed at multiple transects. The results were used to validate the classic model of Circulation in Embracing Sills for Puget Sound and to provide quantitative estimates of the lateral distribution of tidally averaged transport through the system. Sensitivity tests with and without exchanges through Johnstone Strait demonstrate that it is a pathway for Georgia Basin runoff and Fraser River water to exit the Salish Sea and for Pacific Ocean inflow. However the relative impact of this exchange on circulation and flushing in Puget Sound Basin is small.

Bay mussels (Mytilus trossulus) were transplanted to 18 locations representing a range of potential exposures throughout Puget Sound, WA. Tissues were analyzed for over 200 organic contaminants. Results indicated the widespread exposure of marine organisms to trace levels of organic contaminants including the synthetic opioid oxycodone, present at three urban sites, and the chemotherapy drug melphalan, present at nine locations, at levels that may be of biological concern. Land-use and wastewater outfalls were evaluated as potential sources of CECs to the nearshore. Exposure to alkylphenol ethoxylates was associated with increased impervious surfaces in upland watersheds. A hydrodynamic simulation was performed using the Salish Sea Model to integrate inputs from 99 wastewater sources to Puget Sound. Predictions were consistent with concentrations of several wastewater-associated contaminants and δ15N enrichment. These results support the notion that Puget Sound nearshore biota suffer chronic exposures to a suite of contaminants from multiple sources and provide critical to focus future monitoring and management.

Although numerous steady-state effluent plume dilution models are in use, their application in tidal environments remains a challenge. Three-dimensional dynamic circulation models are also inadequate, often due to the lack of required resolution and simplifying assumptions. To overcome these limitations, we present FVCOM-plume-an outfall plume dilution and transport model that operates within the Finite Volume Coastal Ocean Model (FVCOM) framework. It provides simultaneous inclusion of near-field dilution and far-field plume transport processes. The near-field is based on UM3 model using Lagrangian Control Volume approach to compute buoyant plume trajectory and dilution from multiport diffusers. The far-field uses neutrally buoyant particles with point masses and the random walk method to solve unsteady advection-diffusion processes. A density kernel approach is used to compute concentrations at point locations and analyze far-field plume characteristics. The results demonstrate the ability of FVCOM-plume to simultaneously capture near-field and far-field effluent plume dynamics in tidal environments.

The restoration of eelgrass (Zostera marina L.) is a high priority in Puget Sound, Washington, United States. In 2011, the state set a restoration target to increase eelgrass area by 4,200 ha by 2020, a 20% increase over the 21,500 ha then present. In a region as large, dynamic and complex as Puget Sound, locating areas to restore eelgrass effectively and efficiently is challenging. To identify potential restoration sites we used simulation modeling, a geodatabase for spatial screening, and test planting. The simulation model of eelgrass biomass used time series of water properties (depth, temperature, and salinity) output from a regional hydrodynamic model and empirical water clarity data to indicate growth potential. The GIS-based analysis incorporated results from the simulation model, historical and current eelgrass area, substrate, stressors, and shoreline manager input into a geodatabase to screen sites for field reconnaissance. Finally, we planted eelgrass at test sites and monitored survival. We screened 2,630 sites and identified 6,292 ha of highly to very highly suitable conditions for eelgrass—ample area for meeting the 20% target. Test plantings indicated fine-scale data needs to improve predictive capability. We summarized the results of our analysis for the majority of the ~3,220 km of shoreline in Puget Sound on maps to support restoration site selection and planning. Our approach provides a process for identifying and testing potential restoration sites and highlights information needs and management actions to reduce stressors and increase eelgrass area to meet restoration objectives.

Future projections based on the IPCC high emissions scenario RCP8.5 have previously shown that the Pacific Northwest coastal waters will be subjected to altered ocean states in the upwelled shelf waters, resulting in higher primary productivity and increased regions of hypoxia and acidification in the inner estuarine waters such as the Salish Sea. However, corresponding effects on the lower trophic levels and submerged aquatic vegetation have not yet been quantified. Supported by new synoptic field data, explicit coupled simulation of algae, zooplankton, and eelgrass biomass was accomplished for the first time in the Salish Sea. We re-applied the improved model to evaluate future ecological response and examined potential algal species shift, but with the effects of zooplankton production, metabolism, and predation-prey interactions included. We also evaluated the role of eelgrass with respect to potential for improvements to dissolved oxygen and pH levels and as a mitigation measure against hypoxia and ocean acidification. The results re-confirm the possibility that there could be a substantial area-days increase (≈52-fold) in exposure of benthic and near-bed pelagic species to hypoxic waters in 2095. The projections for ocean acidification similarly indicate ≈ 20 -114% increase in exposure to lower pH corrosive waters with aragonite saturation state ΩA

The Pacific Northwest National Laboratory (PNNL) is evaluating the performance of adsorption materials to extract uranium from natural seawater. Testing consists of measurements of the adsorption of uranium and other elements from seawater as a function of time using flow-through columns and a recirculating flume to determine adsorbent capacity and adsorption kinetics. The amidoxime-based polymer adsorbent AF1, produced by Oak Ridge National Laboratory (ORNL), had a 56-day adsorption capacity of 3.9 ± 0.2 g U/kg adsorbent material, a saturation capacity of 5.4 ± 0.2 g U/kg adsorbent material, and a half-saturation time of 23 ± 2 days. The ORNL AF1 adsorbent has a very high affinity for uranium, as evidenced by a 56-day distribution coefficient between adsorbent and solution of log KD,56day = 6.08. Calcium and magnesium account for a majority of the cations adsorbed by the ORNL amidoxime-based adsorbents (61% by mass and 74% by molar percent), uranium is the fourth most abundant element adsorbed by mass an...

Future climate simulations based on the Intergovernmental Panel on Climate Change emissions scenario (A1B) have shown that the Skagit River flow will be affected, which may lead to modification of the estuarine hydrodynamics. There is considerable uncertainty, however, about the extent and magnitude of resulting change, given accompanying sea level rise and site-specific complexities with multiple interconnected basins. To help quantify the future hydrodynamic response, we developed a three-dimensional model of the Skagit River estuary using the Finite Volume Community Ocean Model (FVCOM). The model was set up with localized high-resolution grids in Skagit and Padilla Bay sub-basins within the intermediate-scale FVCOM based model of the Salish Sea (greater Puget Sound and Georgia Basin). Future changes to salinity and annual transport through the basin were examined. The results confirmed the existence of a residual estuarine flow that enters Skagit Bay from Saratoga Passage to the south and exit...

Floating structures such as barges and ships affect near-field hydrodynamics and create a zone of influence (ZOI). Extent of the ZOI is of particular interest due to potential obstruction to and impact on out-migrating juvenile fish. Here, we present an assessment of ZOI from Hood Canal (Floating) Bridge, located within the 110-km-long fjord-like Hood Canal sub-basin in the Salish Sea, Washington. A field data collection program allowed near-field validation of a three-dimensional hydrodynamic model of Hood Canal with the floating bridge section embedded. The results confirm that Hood Canal Bridge, with a draft of 4.6 m covering ~85% of the width of Hood Canal, obstructs the brackish outflow surface layer. This induces increased local mixing near the bridge, causes pooling of water (up-current) during ebb and flood, and results in shadow/sheltering of water (down-current). The change in ambient currents, salinity, and temperature is highest at the bridge location and reduces to background levels with distance from the bridge. The ZOI extends ~20 m below the surface and varies from 2&ndash, 3 km for currents, from 2&ndash, 4 km for salinity, and from 2&ndash, 5 km for temperature before the deviations with the bridge drop to &lt, 10% relative to simulated background conditions without the bridge present.

While ocean acidification was first investigated as a global phenomenon, coastal acidification has received significant attention in recent years, as its impacts have been felt by different socio-economic sectors (e.g., high mortality of shellfish larvae in aquaculture farms). As a region that connects land and ocean, the Salish Sea (consisting of Puget Sound and the Straits of Juan de Fuca and Georgia) receives inputs from many different sources (rivers, wastewater treatment plants, industrial waste treatment facilities, etc.), making these coastal waters vulnerable to acidification. Moreover, the lowering of pH in the Northeast Pacific Ocean also affects the Salish Sea, as more acidic waters get transported into the bottom waters of the straits and estuaries. Here, we use a numerical ocean model of the Salish Sea to improve our understanding of the carbonate system in Puget Sound; in particular, we studied the sensitivity of carbonate variables (e.g., dissolved inorganic carbon, total alkalinity, pH, saturation state of aragonite) to ocean and freshwater inputs. The model is an updated version of our FVCOM-ICM framework, with new carbonate-system and sediment modules. Sensitivity experiments altering concentrations at the open boundaries and freshwater sources indicate that not only ocean conditions entering the Strait of Juan de Fuca, but also the dilution of carbonate variables by freshwater sources, are key drivers of the carbonate system in Puget Sound.

The 11 mile (1.6 km) Swinomish Federal Navigation Channel provides a safe and short passage to fishing and recreational craft in and out of Northern Puget Sound by connecting Skagit and Padilla Bays, US State abbrev., USA. A network of dikes and jetties were constructed through the Swinomish corridor between 1893 and 1936 to improve navigation functionality. Over the years, these river training dikes and jetties designed to minimize sedimentation in the channel have deteriorated, resulting in reduced protection of the channel. The need to repair or modify dikes/jetties for channel maintenance, however, may conflict with salmon habitat restoration goals aimed at improving access, connectivity and brackish water habitat. Several restoration projects have been proposed in the Skagit delta involving breaching, lowering, or removal of dikes. To assess relative merits of the available alternatives, a hydrodynamic model of the Skagit River estuary was developed using the Finite Volume Community Ocean Model (FVCOM). In this paper, we present the refinement and calibration of the model using oceanographic data collected from the years 2006 and 2009 with a focus on the sediment and brackish water transport from the river and Skagit Bay tide flats to the Swinomish Channel. The model was applied to assess the feasibility of achieving the desired dual outcome of (a) reducing sedimentation and shoaling in the Swinomish Channel and (b) providing a direct migration pathway and improved conveyance of freshwater into the Swinomish Channel. The potential reduction in shoaling through site-specific structure repairs is evaluated. Similarly, the potential to significantly improve of brackish water habitat through dike breach restoration actions using the McGlinn Causeway project example, along with its impacts on sediment deposition in the Swinomish Navigation Channel, is examined.

Circulation in typical fjords is characterized by a shallow brackish layer at the surface over a deep long and narrow saltwater column. This surface layer is responsible for the outflow of water from the fjord and is important for flushing of the basin and water quality maintenance. The vertical structure of circulation and transport is known to be easily disrupted, and we postulate that the stability of fjordal circulation may also be vulnerable to impacts from anthropogenic alterations, such as floating structures, which could constrict the mixing and transport in the upper layers of the water column. First, using simplified fjord geometry and a three-dimensional finite volume coastal ocean model (FVCOM), a baseline examination of tidally averaged current profiles in basins with and without sills is presented. The response, varying from a partially mixed estuary regime to classical fjord conditions matches many fjord-like basins such as those in Puget Sound, Washington. The effect of surface obstruction on tidally averaged currents and residence times was then examined by incorporation of a narrow block in the surface layer of the model across the width of the simplified fjord channel such that normal velocity in the horizontal direction was forced to zero. This block approximated the presence of a floating bridge and was further tested using the geometry of Hood Canal, a fjordal sub-basin with a sill in Puget Sound. The results show that tidally averaged mean outflow under the influence of such a constraint at the water surface could be reduced significantly. In the case of Hood Canal, preliminary results indicate that the presence of the floating bridge might have increased the residence times in the basin by 8–13%, which could be an important factor affecting water quality.

Nutrient pollution from rivers, nonpoint source runoff, and nearly 100 wastewater discharges is a potential threat to the ecological health of Puget Sound with evidence of hypoxia in some basins. However, the relative contribu- tions of loads entering Puget Sound from natural and an- thropogenic sources, and the effects of exchange flow from the Pacific Ocean are not well understood. Development of a quantitative model of Puget Sound is thus presented to help improve our understanding of the annual biogeochem- ical cycles in this system using the unstructured grid Finite- Volume Coastal Ocean Model framework and the Integrated Compartment Model (CE-QUAL-ICM) water quality kinet- ics. Results based on 2006 data show that phytoplankton growth and die-off, succession between two species of al- gae, nutrient dynamics, and dissolved oxygen in Puget Sound are strongly tied to seasonal variation of temperature, solar radiation, and the annual exchange and flushing in- duced by upwelled Pacific Ocean waters. Concentrations in the mixed outflow surface layer occupying approximately 5-20 m of the upper water column show strong effects of eutrophication from natural and anthropogenic sources, spring and summer algae blooms, accompanied by depleted nutrients but high dissolved oxygen levels. The bottom layer reflects dissolved oxygen and nutrient concentrations of upwelled Pacific Ocean water modulated by mixing with biologically active surface outflow in the Strait of Juan de Fuca prior to entering Puget Sound over the Admiralty Inlet. The effect of reflux mixing at the Admiralty Inlet sill result- ing in lower nutrient and higher dissolved oxygen levels in bottom waters of Puget Sound than the incoming upwelled Pacific Ocean water is reproduced. By late winter, with the reduction in algal activity, water column constituents of interest, were renewed and the system appeared to reset with cooler temperature, higher nutrient, and higher dissolved oxygen waters from the Pacific Ocean.

Due to increased pollutant loads and water use from coastal development and population growth, occurrences of low-dissolved oxygen and ''hypoxic zones'' have increased. Reports of fish kills and water quality impairment are also becoming more frequent in many coastal waters. Water quality managers and regulatory agencies rely on numerical modeling tools to quantify the relative contributions of anthropogenic and ''natural'' pollutant loads (nutrients and biochemical oxygen demand) on dissolved oxygen levels and use the results for remedial activities and source control. The ability to conduct season-long simulations with sufficient nearshore resolution is therefore a key requirement. Mesh flexibility and the ability to increase site specific resolution without disturbing the larger domain setup and calibration are critical. The objective of this effort was to develop a robust biogeochemical model suitable for simulation of water quality dynamics including dissolved oxygen in complex coastal environments with multiple tidal channels, tidal flats, and density-driven circulation using unstructured-grid formulation. This paper presents an offline unstructured biogeochemical model that uses the Finite Volume Coastal Ocean Model (FVCOM) discretization of the study domain and the corresponding hydrodynamic solution to drive biogeochemical kinetics based on a water quality model CE-QUAL-ICM. In this paper, the linkage between selected hydrodynamic and water quality models is subjected to several scalar transport and biogeochemical module tests (plume transport and dilution, BOD/DO sag, and phytoplankton/nutrients reaction), and results are compared to their analytical solutions as part of model validation. A preliminary application of the biogeochemical model with a year-long simulation of Hood Canal basin in Puget Sound, USA, is presented as an example and a test of the tool in a real estuary setting. The model reproduced the dynamics and seasonal variations in the biogeochemical state variables and was used to test short-term wind-driven dynamics that could influence dissolved oxygen concentrations in Hood Canal.

The interactions of physical processes between estuaries and upstream river floodplains are of great importance to the fish habitats and ecosystems in coastal regions. Traditionally, a hydraulic analysis of floodplains has used one- or two-dimensional models. While this approach may be sufficient for planning the engineering design for flood protection, it is inadequate when floodwaters inundate the floodplain in a complex manner. Similarly, typical estuarine and coastal modeling studies do not consider the effect of upstream river floodplains because of the technical challenge of modeling wetting and drying processes in floodplains and higher bottom elevations in the upstream river domain. While various multi-scale model frameworks have been proposed for modeling the coastal oceans, estuaries, and rivers with a combination of different models, this paper presents a modeling approach for simulating the hydrodynamics in the estuary and river floodplains, which provides a smooth transition between the two regimes using an unstructured-grid, coastal ocean model. This approach was applied to the Skagit River estuary and its upstream river floodplain of Puget Sound along the northwest coast of North America. The model was calibrated with observed data for water levels and velocities under low-flow and high-flood conditions. This study successfully demonstrated that a three-dimensional estuarine and coastal ocean model with an unstructured-grid framework and wetting-drying capability can be extended much further upstream to simulate the inundation processes and the dynamic interactions between the estuarine and river floodplain regimes.

Through extensive field data collection and analysis efforts conducted since the 1950s, researchers have established an understanding of the characteristic features of circulation in Puget Sound. The pattern ranges from the classic fjordal behavior in some basins, with shallow brackish outflow and compensating inflow immediately below, to the typical two-layer flow observed in many partially mixed estuaries with saline inflow at depth. An attempt at reproducing this behavior by fitting an analytical formulation to past data is presented, followed by the application of a three-dimensional circulation and transport numerical model. The analytical treatment helped identify key physical processes and parameters, but quickly reconfirmed that response is complex and would require site-specific parameterization to include effects of sills and interconnected basins. The numerical model of Puget Sound, developed using unstructured-grid finite volume method, allowed resolution of the sub-basin geometric features, including presence of major islands, and site-specific strong advective vertical mixing created by bathymetry and multiple sills. The model was calibrated using available recent short-term oceanographic time series data sets from different parts of the Puget Sound basin. The results are compared against 1) recent velocity and salinity data collected in Puget Sound from 2006 and 2) a composite data set from previously analyzed historical records, mostly from the 1970s. The results highlight the ability of the model to reproduce velocity and salinity profile characteristics, their variations among Puget Sound sub-basins, and tidally averaged circulation. Sensitivity of residual circulation to variations in freshwater inflow and resulting salinity gradient in fjordal sub-basins of Puget Sound is examined.

Estuarine and coastal hydrodynamic processes are sometimes neglected in the design and planning of nearshore restoration actions. Despite best intentions, efforts to restore nearshore habitats can result in poor outcomes if water circulation and transport are not properly addressed. Land use constraints can lead to selection of suboptimal restoration alternatives that may result in undesirable consequences, such as flooding, deterioration of water quality, and erosion, that require immediate remedies and costly repairs. Quantitative models designed for application to the nearshore environment can minimize uncertainty about restoration goals, such as recovery of tidal exchange, supply of sediment and nutrients, and establishment of fish migration pathways. A high-resolution circulation and transport model of the Puget Sound, in the state of Washington, was developed based on an unstructured grid framework to define the complex shoreline using a finite volume coastal ocean model. The Puget Sound model is intended to assist with nearshore habitat restoration design and analysis, and to answer the question, “Can we achieve beneficial restoration outcomes at small scale, as well as estuary-wide?” Examples of restoration projects in the area illustrate the model’s capacity to simulate important nearshore processes such as circulation in complex multiple tidal channels, wetting and drying of tide flats, and water quality and sediment transport.

Past dike placement for agriculture has considerably altered the Grays River, Washington, a tributary to the Columbia River, and impaired anadramous salmon habitat. To improve floodplain connectivity, a wetland restoration project was implemented during the summer of 2005 at the Kandoll Farm restoration site (KFS) along the Grays River. This project included breaching the dikes at three locations, installing large culverts at the head of Seal Slough, and altering the access road elevations. The following winter, in January 2006, high flows in the Grays River produced extreme flooding conditions, overtopping dikes along the river and roads upstream of the KFS. We developed a two-dimensional unstructured-grid hydrodynamic model to evaluate the flooding conditions prior to restoration construction (Pre) and following restoration construction activities (Post). In our analyses at the time of peak water surface elevations (WSE), we found no reduction in peak WSE at the KFS in comparisons between the Pre and Post configurations, and the Post analyses showed a slight increase in WSE within the Grays River channel in comparison to the Pre analysis. Following the passage of the January 2006 flood, the Post WSEs within the KFS and in the main river channel were lower than the Pre WSEs. The velocity at a cross section of the Grays River upstream of KFS did not change between the Post and Pre configurations, but within KFS and at a cross section downstream, there were significant differences in velocities. We attributed the changes to better drainage from the KFS and improved connectivity with the main river channel resulting from the restoration project.

Water circulation in Puget Sound, a large complex estuary system in the Pacific Northwest coastal ocean of the United States, is governed by multiple spatially and temporally varying forcings from tides, atmosphere (wind, heating/cooling, precipitation/evaporation, pressure), and river inflows. In addition, the hydrodynamic response is affected strongly by geomorphic features, such as fjord-like bathymetry and complex shoreline features, resulting in many distinguishing characteristics in its main and sub-basins. To better understand the details of circulation features in Puget Sound and to assist with proposed nearshore restoration actions for improving water quality and the ecological health of Puget Sound, a high-resolution (around 50 m in estuaries and tide flats) hydrodynamic model for the entire Puget Sound was needed. Here, a three-dimensional circulation model of Puget Sound using an unstructured-grid finite volume coastal ocean model is presented. The model was constructed with sufficient resolution in the nearshore region to address the complex coastline, multi-tidal channels, and tide flats. Model open boundaries were extended to the entrance of the Strait of Juan de Fuca and the northern end of the Strait of Georgia to account for the influences of ocean water intrusion from the Strait of Juan de Fuca and the Fraser River plume from the Strait of Georgia, respectively. Comparisons of model results, observed data, and associated error statistics for tidal elevation, velocity, temperature, and salinity indicate that the model is capable of simulating the general circulation patterns on the scale of a large estuarine system as well as detailed hydrodynamics in the nearshore tide flats. Tidal characteristics, temperature/salinity stratification, mean circulation, and river plumes in estuaries with tide flats are discussed.

Along the Pacific Northwest coast, much of the estuarine habitat has been lost over the last century to agricultural land use, residential and commercial development, and transportation corridors. As a result, many of the ecological processes and functions have been disrupted. To protect and improve these coastal habitats that are vital to aquatic species, many projects are currently underway to restore estuarine and coastal ecosystems through dike breaches, setbacks, and removals. Understanding site-specific information on physical processes is critical for improving the success of such restoration actions. In this study, a three-dimensional hydrodynamic model was developed to simulate estuarine processes in the Stillaguamish River estuary, where restoration of a 160-acre parcel through dike setback has been proposed. The model was calibrated to observed tide, current, and salinity data for existing conditions and applied to simulate the hydrodynamic responses to two restoration alternatives. Model results were then combined with biophysical data to predict habitat responses within the restoration footprint. Results showed that the proposed dike removal would result in desired tidal flushing and conditions that would support four habitat types on the restoration footprint. At the estuary scale, restoration would substantially increase the proportion of area flushed with freshwater (

Many nearshore restoration projects are currently underway at coastal locations where human influence and development have disrupted natural habitat and coastal ecological systems. The objectives of these projects in general are to restore the lost estuarine functions to the tidal marshland. Often these projects are conducted with little understanding of the potential effects of other nearby projects within the ecosystem, and similarly, it is easy to neglect the effect of the local project on the larger estuarine scale. In this paper, a modeling study is presented to evaluate the hydrodynamic responses of multiple restoration projects and their cumulative effect in the Snohomish River estuary in Washington, USA. The concept of absolute mean tidal transport is introduced and used to measure the cumulative effect of the proposed restoration projects on the estuarine hydrodynamics. The results show that the hydrodynamic responses due to multiple restoration projects are additive in the estuary, and the effect is nonlinear. The hydrodynamic response under restoration conditions depends on the size of the restoration area and the geometric configuration of the existing river channels. Within a complex braided estuary such as the Snohomish, the influence of a specific restoration project is not only experienced locally, but also found to significantly affect tidal transport in all distributary branches within the system.

Tidal circulation and river plume dynamics in shallow-water estuarine systems with large intertidal zones are complex. Strong asymmetries in tidal currents and stratification often occur in the intertidal zones and subtidal channels over a tidal cycle. The Skagit River is the largest estuary with respect to the discharge of a significant amount of freshwater and sediment into Puget Sound, Washington. It consists of a large intertidal zone with multiple tidal channels near the mouth of the estuary. To simulate the tidal circulation and salinity stratification accurately in the intertidal region, an unstructured grid numerical model with wetting–drying capability and the capability to accurately represent the bathymetry of tidal flats and the geometry of shallow distributary channels is necessary. In this paper, a modeling study for the Skagit River estuary using a three-dimensional unstructured grid, finite-volume coastal ocean model (FVCOM) supported by high-resolution LIDAR data is presented. The hydrodynamic model was validated with observed water surface elevation, velocity, and salinity data over spring and neap tidal cycles under low-river-flow and high-river-flow conditions. Wetting and drying processes in the intertidal zone and strong stratification in the estuary were simulated successfully by the model. Model results indicate that the Skagit River estuary is a highly stratified estuary, but destratification can occur during flood tide. Tides and baroclinic motion are the dominant forcing in the Skagit River estuary, but strong wind events can affect the currents in the intertidal zone significantly. Preliminary analysis also indicated that the salinity intrusion length scale is proportional to the river flow to the −¼ power.

The Snohomish River is one of the largest rivers to discharge into to the Puget Sound estuarine system. The tidal circulation, mixing and salt intrusion processes in the Snohomish River estuary are complex due to the presence of a large intertidal region, multiple distributary channels, and a sharp gradient of bottom elevation from the estuary to the fjordal depths of Puget Sound. To accurately simulate the tidal mixing and salt intrusion in such a complex system, a high-resolution model grid in both horizontal and vertical directions is required to represent the details of the geometry and bathymetry changes in the study domain. In this paper, a finite volume, unstructured coastal ocean model, FVCOM, was used to simulate the estuarine physical processes specific to the current state of the Snohomish River estuary, which consists of a number of dike-trained channels forming a uniquely braided system. The model was calibrated against observed data for a neap-spring tidal cycle collected during fal...

Hydropower reservoirs impounded by high-head dams exhibit complex circulation that confuses the downstream migrating salmon and limits successful collection and passage of fish. Fish passage engineers attempt to modify the hydrothermal behavior at reservoirs through structural and operational modifications and often use hydrodynamic simulations to guide their actions. Simulation of key hydrothermal processes such as (a) development of a stable two-layer stratified system, (b) density-driven currents over a reservoir length scale, and (c) discharge hydraulics near the power generation and fish collection intakes requires highly specialized models applied at differing temporal and spatial scales. A staged modeling approach is presented that uses external coupling of models at varying temporal scales and spatial resolution to simulate the entire hydraulic regime from the mouth of the reservoir at the upstream end to the discharge at the dam. The staged modeling approach is illustrated using a case s...

A three-dimensional Reynolds-averaged Navier–Stokes computational fluid dynamics (CFD) model is developed for simulating initial mixing in the near field of thermal discharges at real-life geometrical configurations. The domain decomposition method with multilevel embedded overset grids is employed to handle the complexity of real-life diffusers as well as to efficiently account for the large disparity in length scales arising from the relative size of the ambient river reach and the typical diffuser diameter. An algebraic mixing length model with a Richardson-number correction for buoyancy effects is used for the turbulence closure. The governing equations are solved with a second-order-accurate, finite-volume, artificial compressibility method. The model is validated by applying it to simulate thermally stratified shear flows and negatively buoyant wall jet flows and the computed results are shown to be in good overall agreement with the experimental measurements. To demonstrate the potential of the num...

Dams and reservoir operations modify natural stream behaviour and affect the downstream characteristics such as mean temperatures and diurnal temperature amplitudes. Managing phase effects due to reservoir operation and the associated amplification of daily maximum temperatures in the downstream reaches remains a challenge. An analytical approach derived from a one-dimensional heat advection and dispersion equation with surface heating in the form of equilibrium temperature was developed to examine the potential for restoration of natural stream temperatures. The analytical model was validated with observed temperature data collected in the Clackamas River, Oregon, and was used to highlight key downstream temperature behaviour characteristics. Mean stream temperatures below the dam are relatively stable and upon deviating from natural stream mean temperatures, return asymptotically to their natural state. In contrast, the amplitudes of daily temperature variation are highly sensitive to the phase differences induced by the dam and could nearly double in natural amplitude within the first 24 h. The analysis showed that restoring average stream temperatures to natural levels through structural and operational modifications at the dam may not be sufficient as phase-induced temperatures maximums would continue to persist.

Nutrient levels in coastal waters must be accurately assessed to determine the nutrient effects of increasing populations on coastal ecosystems. To accomplish this goal, in-field data with sufficient temporal resolution are required to define nutrient sources and sinks, and to ultimately calculate nutrient budgets. Models then are required for the interpretation and analysis of data sets. To quantify the coastal ocean nitrogen input to Yaquina Bay, Oregon, nitrate concentrations were measured by a moored sensor hourly for one month during summer upwelling some distance outside the estuary entrance jetties. The time series results then were interpreted using a steady state model (Visual Plumes’ PDSW) and a hydrodynamic model, the Finite Volume Coastal Ocean Model (FVCOM). The physical scales of many stream and river plumes often lie between the scales for outfall mixing zone plume models, such as those found in EPA's Visual Plumes, and larger-sized grid scales for regional circulation models like FVCOM. A potential advantage of relatively simple, steady state plume models is that they use entrainment terms to close the plume equations, theory that has proven useful in simulating turbulent plume discharges from various sources, some approaching the dimensions of rivers. Important advantages of models like FVCOM are that they are dynamic and include the effects of the Earth's rotation. The results showed that the steady-state plume model simulates observed velocity and concentration data fairly well during periods of strong discharge velocity and weak ambient coastal currents. FVCOM was judged to give better estimates under all other ambient current conditions, although the data from the mooring cannot be used to prove this assertion as stronger currents would deflect the plume away from the mooring. Nevertheless, plume models may be useful in establishing boundary and initial conditions for hydrodynamic models.

Pronounced stratification and peaking operation, typical of reservoirs impounded by high-head dams, result in complex current patterns. These cause disorientation in downstream migrating salmon and interfere with downstream passage. Structural and operational modifications such as installations of curtains, surface withdrawal, draw down, and selective withdrawal are often considered to alter the stratification and modify the currents to enhance the movement of fish toward the forebay where they may be collected effectively. Effectiveness of design modification in deep reservoirs is highly dependent on site-specific hydraulic and meteorological conditions, and numerical models are the tools of choice in design and selection of the optimum alternative. Although most hydropower reservoirs exhibit a vertical-longitudinal 2-D current structure, 3-D flow patterns are prevalent in reservoirs with multiple branches, and they occur near the power intakes as well. Simulation of these currents requires a 3-...

The Salish Sea, including Puget Sound, is a large estuarine system bounded by over seven thousand miles of complex shorelines, consists of several subbasins and many large inlets with distinct properties of their own. Pacific Ocean water enters Puget Sound through the Strait of Juan de Fuca at depth over the Admiralty Inlet sill. Ocean water mixed with freshwater discharges from runoff, rivers, and wastewater outfalls exits Puget Sound through the brackish surface outflow layer. Nutrient pollution is considered one of the largest threats to Puget Sound. There is considerable interest in understanding the effect of nutrient loads on the water quality and ecological health of Puget Sound in particular and the Salish Sea as a whole. The Washington State Department of Ecology (Ecology) contracted with Pacific Northwest National Laboratory (PNNL) to develop a coupled hydrodynamic and water quality model. The water quality model simulates algae growth, dissolved oxygen, (DO) and nutrient dynamics in Puget Sound to inform potential Puget Sound-wide nutrient management strategies. Specifically, the project is expected to help determine 1) if current and potential future nitrogen loadings from point and non-point sources are significantly impairing water quality at a large scale and 2) what level of nutrient more » reductions are necessary to reduce or control human impacts to DO levels in the sensitive areas. The project did not include any additional data collection but instead relied on currently available information. This report describes model development effort conducted during the period 2009 to 2012 under a U.S. Environmental Protection Agency (EPA) cooperative agreement with PNNL, Ecology, and the University of Washington awarded under the National Estuary Program « less