Sediment Transport Into the Swinomish Navigation Channel, Puget Sound—Habitat Restoration Versus Navigation Maintenance Needs

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Journal of Marine Science and Engineering

Article Sediment Transport into the Swinomish Navigation Channel, Puget Sound—Habitat Restoration versus Navigation Maintenance Needs

Tarang Khangaonkar 1,*, Adi Nugraha 1, Steve Hinton 2, David Michalsen 3 and Scott Brown 3

1 Paciﬁc Northwest National Laboratory, Seattle, WA 98109, USA; [email protected] 2 Skagit River System Cooperative, La Conner, WA 98257, USA; [email protected] 3 U.S. Army Corps of Engineers, P.O. Box 3755, Seattle, WA 98124, USA; [email protected] (D.M.); [email protected] (S.B.) * Correspondence: [email protected]; Tel.: +1-206-528-3053

Academic Editor: Zeki Demirbilek Received: 26 February 2017; Accepted: 12 April 2017; Published: 21 April 2017

Abstract: 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.

Keywords: hydrodynamics; sediment transport; nearshore restoration; dredging; dike alteration; FVCOM; Puget Sound; Salish Sea

1. Introduction The Swinomish Navigation Channel is located near the mouth of the Skagit River estuary, which is the largest river in the Salish Sea estuarine system consisting of Puget Sound, Strait of Juan De Fuca, and Georgia Strait (Figure1a). The Skagit River estuary is a macro-tidal environment with a tidal range of 4 m and ﬂuctuations around −1 to 3 m during spring tide and −0.5 to 2.5 m during neap tide relative to NAVD88. It has mixed semi-diurnal and diurnal tidal forcing and signiﬁcant diurnal inequalities. The Skagit drainage basin delivers approximately 39 percent of the total sediment discharged to Puget Sound [1] and could, at times, account for more than 50 percent of the freshwater

J. Mar. Sci. Eng. 2017, 5, 19; doi:10.3390/jmse5020019 www.mdpi.com/journal/jmse J. Mar. Sci. Eng. 2017, 5, 19 2 of 22 inflow [2]. The Skagit River Delta provides rich estuarine and freshwater habitats for salmon and many other fish and wildlife species. Over the past 150 years, economic development in the Skagit River Delta has resulted in significant losses of fish and wildlife habitat and alteration of habitat sustaining processes, particularly resulting from the construction of dikes and levees for agricultural land use. The dikes have impeded fish passages through the area and greatly reduced nursery habitat for many fish and invertebrate species [3]. The dikes have also diverted freshwater away from the dike-front region that was historically a productive brackish marsh that fostered alongshore habitat connectivity. Therefore, marsh habitat has been lost, and the dike-front region has deteriorated into tide-flat conditions with increased salinity (20 to 25 ppt) devoid of vegetation. In response, several habitat restoration projects/alternatives have been proposed in this basin. The 2006 Skagit Chinook Recovery Plan identified a total of 26 nearshore restoration opportunities in the Skagit delta [4]. These projects strive to restore hydrologic and hydrodynamic functions in the tidal marshlands largely through shoreline modifications such as dike breaching, dike setback, and dike removal. The numeric criteria for restoration-site hydrodynamic performance are species specific, vary from site to site, and are typically categorized in broad rules such as (a) desired minimum inundation depth and frequency (e.g., >0.3 m and >50% of time); (b) salinity range (e.g., 5–15 ppt); and (c) peak velocity (e.g., <0.5 m/s). A series of engineering activities have also occurred associated with the development of the Swinomish (Navigation) Channel. It is a 11 mile (1.6 km) long, 100-foot (30.5 m) wide, and 12 feet (3.7 m or 4.6 m/NAVD88) deep channel between Skagit Bay to the south and Padilla Bay to the north that was initially completed in in 1936. Once constructed, the project established short and safe route for vessels traveling between inner Puget Sound and the Straits of Georgia and Juan De Fuca (see Figure1b). For Skagit River, which is the largest of Puget Sound tributaries that supplies approximately 2.8 million tons of sediment per year to the Skagit Bay [5], shoaling in the Swinomish channel has always been an issue. To secure navigability through this corridor, four training structures were constructed to confine flows and impede sediments from entering the Swinomish Channel from the Skagit River North Fork delta. Figure1b shows the Skagit River Estuary study area along with the Swinomish Channel and the training structures. In recent years, functionality of the navigation features of the Swinomish Channel has deteriorated due to excessive shoaling. The reliability of the channel is tied to the condition of the navigation training structures designed to minimize shoaling. These dikes have deteriorated and undergone several modifications. Recent condition surveys (2014) indicate that channel depths are less than 5 feet (1.5 m or 2.4 m/NAVD88) below mean lower low water (MLLW) at certain locations in the reach between Skagit Bay and McGlinn Island. The U.S. Army Corps of Engineers (USACE) responsible for maintenance of the navigation channel is currently investigating alternatives to reduce the operations and maintenance (O&M) dredging demands over the next 50 years. Construction of the Swinomish Channel and the associated jetty and dikes have changed this waterway from a highly complex, braided deltaic distributary wetland to a simplified channel bounded by dikes. These changes have also resulted in loss of connectivity between habitat forming processes and functions associated with freshwater flows of the Skagit River and the estuarine transitioning environment of the Swinomish Channel to Skagit and Padilla Bays. Detailed understanding of the circulation and hydrodynamic conditions in the Skagit River estuary, and its interaction with Padilla Bay to the north and Saratoga Passage to the south are only beginning to emerge through short-duration synoptic measurements of currents, tides, salinities, and temperatures [6–8]. A three-dimensional (3D) hydrodynamic model of the Skagit River estuary including Skagit Bay, the North Fork, the connection to Padilla Bay through Swinomish Channel, and the braided network associated with the South Fork was developed previously to assist with restoration feasibility assessments [9]. The model was developed using the Finite Volume Coastal Ocean Model (FVCOM) code [10], and includes a detailed representation of the tide flat bathymetry, river-training dikes and jetty, Swinomish Channel, and Skagit Bay. J. Mar. Sci. Eng. 2017, 5, 19 3 of 22 J. Mar. Sci. Eng. 2017, 5, 19 3 of 22

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Figure 1. Study area showing, (a) Northern Puget Sound area and (b) Swinomish Channel near the Figure 1. Study area showing, (a) Northern Puget Sound area and (b) Swinomish Channel near the mouth of Skagit River estuary, located in Whidbey Basin, Puget Sound, Washington. (A) North Dike; mouth of Skagit River estuary, located in Whidbey Basin, Puget Sound, Washington. (A) North Dike; (B) McGlinn Island to Goat Island Jetty; (C) South Jetty; (D) McGlinn Island to Mainland causeway, (B) McGlinn Island to Goat Island Jetty; (C) South Jetty; (D) McGlinn Island to Mainland causeway, (E) McGlinn Island. (E) McGlinn Island.

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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 primary objective is to develop the model for use in the design of repair and modifications to structures to improve the reliability of the Swinomish Channel. However, the availability of the model also allows examination of potential opportunities for 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. A sensitivity test style application of the model is presented using two dike modification scenarios for a comparative assessment. The feasibility of achieving desired outcome of reduction in shoaling through site-specific jetty repairs is analyzed. Similarly, potential to increase sediment deposition due to dike breach restoration scenarios at McGlinn Causeway project site is also examined. Despite best intentions, efforts to restore near-shore habitats can result in poor outcomes for area land uses and local community infrastructure if water circulation and sediment transport are not properly addressed. Response of natural processes to physical changes are often nonlinear, and land-use constraints can lead to selection of restoration alternatives that may result in undesirable consequences for the built environment, such as flooding, deterioration of water quality, and erosion, that require immediate remedies and costly repairs. In the case of Swinomish Channel, the projects could lead to increased sedimentation and maintenance dredging. Through this case study, we demonstrate the feasibility and importance of using large-scale (estuary-wide) 3D hydrodynamic and sediment transport models with local refinements down to fine scale (10 m dike sections) for assessment of and design shoreline modification projects. While FVCOM hydrodynamic model has been used extensively over the world its application for sediment transport and use for habitat restoration are relatively new. The contribution of this paper is the demonstration that FVCOM-sediment transport module may be used effectively in support of nearshore restoration and shoreline modification assessment to address feasibility concerns related to sedimentation along with other hydrodynamic processes.

2. Materials and Methods For this study, we selected data from a survey in 2006 during which numerous stations in the Swinomish Channel region pertinent to this assessment were available. Oceanographic data was collected at several locations in Skagit Bay and the Swinomish Channel by U.S. Geological Survey (USGS) from 1 May 2006 to 31 May 2006 [8]. Additional data was also collected in 2009, as part of an Office of Naval Research sponsored effort to study sediment transport over tidal flats when Woods Hole Oceanographic Institute (WHOI) [11] conducted an extensive field campaign with fixed and shipboard observations. This study was designed for high-resolution measurements of current profiles, salinity, temperature, and acoustic and optical back scatter. Suspended sediment concentrations (SSC) measured from the surface and bottom layers were used to calibrate optical and acoustic sensors. This data and the associated sediment transport model from WHOI study were selected for use in this assessment. The approach was to first improve the model grid and domain coverage, upgrade the bathymetric representation using latest surveys and calibrate the hydrodynamic model to data from the 2006 USGS survey. Following hydrodynamic calibration, conduct the model setup for Year 2009 conditions corresponding to WHOI data collection period and complete the sediment transport model validation.

2.1. Hydrodynamic Model of the Skagit River Estuary with the Swinomish Channel An improved version of the hydrodynamic model of the Skagit River estuary by Yang and Khangaonkar [9,11] was used in this study. The model uses ﬁnite volume community ocean model (FVCOM) code [12] and solves the three-dimensional momentum, continuity, temperature, salinity, and density equations in an integral form by computing ﬂuxes between non-overlapping, horizontal, J. Mar. Sci. Eng. 2017, 5, 19 5 of 22

andJ. Mar. triangular Sci. Eng. control2017, 5, 19 volumes. A 30-layer sigma-stretched coordinate system was used in the vertical5 of 22 plane with unstructured triangular cells in the lateral plane. The model employs the Mellor Yamada level-2.5Mellor turbulent Yamada closurelevel-2.5 scheme turbulent for closurevertical scheme mixing [ for12] vertical and the mixing Smagorinsky [12] and scheme the Smagorinsky for horizontal mixingscheme [13 ]. for The horizontal original modelmixing of [13]. Skagit The River original estuary model was of improved Skagit River through estuary grid was refinement improved and domainthrough expansion grid refineme to allownt better and domain characterization expansion of to the allow exchange better between characterization Skagit Bay of andthe exchangePadilla Bay throughbetween the Skagit Swinomish Bay and Channel. Padilla The Bay high-resolution through the Swinomish grid refinement Channel. focused The primarily high-resolution on the gridmarsh habitatrefinement and tidal focused flat regions, primarily including on the marsh restoration habitatsites. and tidal To simulate flat regions, the tidal-waveincluding restorat propagationion sites. and To simulate the tidal-wave propagation and salinity intrusion properly in the multi-channel and salinity intrusion properly in the multi-channel and tide-flat area, finer grid cells were specified in tide-flat area, finer grid cells were specified in the intertidal channels, the marshlands near the the intertidal channels, the marshlands near the habitat restoration sites, and between the tributary habitat restoration sites, and between the tributary sloughs. The prior model domain of Skagit sloughs. The prior model domain of Skagit Estuary was expanded to include Padilla Bay through the Estuary was expanded to include Padilla Bay through the connection of the Swinomish Channel to connection of the Swinomish Channel to Skagit Bay. Like Skagit Bay, a large tide flat important for Skagit Bay. Like Skagit Bay, a large tide flat important for providing near-shore fish habitat exists in providingPadilla Ba near-shorey. To represent fish habitat the Padilla exists Bay in Padillatide flats Bay. accurately, To represent we obtained the Padilla detailed Bay tidebathymetric flats accurately, data wethat obtained had been detailed compiled bathymetric by Western data that Washington had been University compiled by (WWU) Western based Washington on historical University data (WWU)collected based by onthe historicalNational Oceanic data collected and Atmospheric by the National Administration Oceanic and (NOAA) Atmospheric by the National Administration Ocean (NOAA)Service by and the the National historic Ocean U.S. Coast Service and and Geodetic the historic Survey. U.S. Bathymetric Coast and data Geodetic collected Survey. for the Bathymetric Padilla dataBay collected National for Estuarine the Padilla Research Bay National Reserve Estuarinewas applicable Research to the Reserve Fidalgo was Bay applicable region. A to navigation the Fidalgo Baychannel region. appearing A navigation to be channela dredged appearing extension to of be the a dredgedSwinomish extension Channel ofexists the Swinomishin the shallow Channel tide existsflats in region the shallow in Padilla tide Bay flats and region has also in been Padilla incorporated Bay and has in the also model been geometry. incorporated The inmodel the modelgrid geometry.was constructed The model with grid details was constructedto resolve such with key details features to resolveas well suchas other key main features tidal as channels well as other in mainPadilla tidal Bay. channels The intertidal in Padilla bathymetry Bay. The intertidal near the bathymetry mouth of the near North the mouth Fork of of Skagit the North River Fork was of Skagitupdated River using was a updated combination using of aLidar combination data and ofboat Lidar-based data surveys and boat-basedconducted by surveys USACE conducted and USGS by USACEin 2012 and and USGS 2014. in Figure 2012 and 2a below 2014. shows Figure the2a below Skagit shows River estuary the Skagit model River with estuary a closeup model of with the a closeupSwinomish of the Channel Swinomish region. Channel The updated region. The model updated grid model has 26,248 grid hasnodes 26,248, 59,329 nodes, elements 59,329 and elements 30 andsigma 30 sigma-layers.-layers.

(a) (b)

Figure 2. (a) The Skagit River estuary model grid with expanded domain covering Padilla Bay to the Figure 2. (a) The Skagit River estuary model grid with expanded domain covering Padilla Bay to north and Saratoga Passage to the South with the Swinomish Channel connecting the two basins; (b) the north and Saratoga Passage to the South with the Swinomish Channel connecting the two basins; the locations of May 2006 (blue circles), WHOI study mooring stations during June of 2009 [13] (b) the locations of May 2006 (blue circles), WHOI study mooring stations during June of 2009 [13] (green diamonds), and for scenario evaluation (red circles). (green diamonds), and for scenario evaluation (red circles). As a first step, the performance of the model with the refined grid in the Swinomish Channel region was tested against the data from the Swinomish Channel region collected in 2006 by USGS

J. Mar. Sci. Eng. 2017, 5, 19 6 of 22

As a first step, the performance of the model with the refined grid in the Swinomish Channel region was tested against the data from the Swinomish Channel region collected in 2006 by USGS [8]. Skagit River inflow data were obtained from a USGS stream gage about 25 km upstream of the estuarine mouth, at Mt. Vernon, WA, USA. Wind data were obtained from University of Washington Weather Research and Forecasting results. We used spatially uniform wind magnitude and direction for wind forcing. Tidal elevations at the model open boundaries at Saratoga Passage, Deception Pass/Bowman Bay, Guemez Channel/Anacortes, and Chucknaut/Padilla Bay were obtained from a harmonic tide prediction software (XTIDE) based on NOAA’s National Oceanic Service algorithms (http://www.flaterco.com/xtide/). Figure3 shows a comparison of observed and simulated currents at two of the Swinomish Channel locations along with tides and salinity. Model performance was evaluated using error statistics such as absolute mean error (AME), root-mean-square error (RMSE) and model skill (SS) (Table1). The AME and RMSE of time series with N elements are defined as

1 AME = |(X − X )| (1) N ∑ mdl obs s 2 ∑(X − X ) RMSE = mdl obs (2) N Model skill metric was adopted from Willmott [14] and is deﬁned as

2 ∑(X − X ) SS = 1 − mdl obs (3) 2 ∑ Xmdl − Xobs + Xobs − Xobs where Xmdl and Xobs are the values from the model and observations, and an overbar represents a time average. Primary conclusion from this initial effort was that grid resolution and bathymetry in the Swinomish Channel region were sufﬁcient to reproduce observed currents for use in sediment transport modeling. Error statistics are shown in Table1 below. Note that his preliminary application was conducted using 10 layers. To improve salinity predictions and near-bed shear stress, a 30-layer model setup was selected for the setup and calibration of the sediment transport model presented in the next section.

Table 1. Hydrodynamic model calibration error statistics, May 2006.

Water Surface Level, m Velocity, m/s Salinity, ppt Station AME 1 RMSE 2 SS 3 AME RMSE SS 3 AME RMSE SS 3 u 3:0.20; u:0.24; 0.85 S1 – – –– v:0.29 v:0.32 0.84 u:0.32; u:0.37; 0.60 S2 – – –– v:0.34 v:0.42 0.52 S3 – – – – 2.40 3.16 0.40 S4 0.31 0.38 0.96 – – 1.73 2.24 0.42 u:0.34; u:0.42; 0.55 S5 0.32 0.39 0.95 –– v:0.22 v:0.26 0.77 S6 0.26 0.32 0.94 – – – – 1 AME = absolute mean error, 2 RMSE = root mean square error, 3 SS = skill score, u and v are velocity components in the x and y (east and north) directions respectively.

Not included in this table are model bias values for currents that were relatively small and varied from −0.02 m/s to 0.08 m/s for “u” and “v” components at stations S1, S2, and S5. J. Mar. Sci. Eng. 2017, 5, 19 7 of 22 J. Mar. Sci. Eng. 2017, 5, 19 7 of 22

Figure 3. Comparison of observed tide, salinity, and currents in the Swinomish Channel (Figure 22b)b) shown asas exampleexample at at stations stations S1, S1, S2, S2, and and S4 S4 during during May May of 2006 of 2006 as part as ofpart hydrodynamic of hydrodynamic model model setup setupand calibration. and calibration.

2.22.2.. Sediment Transport Model ofof thethe SkagitSkagit RiverRiver EstuaryEstuary withwith thethe SwinomishSwinomish ChannelChannel

2.2.12.2.1.. Skagit River Sediment Load and Deposition Characteristics USGS maintains a permanent monitoring gage at Mt. Vernon, Vernon, Washington (USGS 12200500) on the mainstream of SkagitSkagit River, locatedlocated at River Miles (RM)(RM) 15.7. Strong daily flow flow variation in river flowflow is observed and is attributed to daily peaking mode operations at the upstream hydropower projects. To To facilitate facilitate analysis analysis over over a long a long period period representative representat ofive current of current conditions, conditions, a 24 year a 24 record year recordof flow of data flow was data extracted was extracted from the from Mt. the Vernon Mt. Vernon gagearchives. gage archives. During During this period, this period, the highest the highest flow flowrecorded recorded was 142,000was 142, cubic000 cubic feet per feet second per second (cfs) (4024(cfs) (4024 m3/s) m that3/s) that occurred occurred in November in November of 1990, of 1990, and andthe lowestthe lowest flow flow was 3600was 3 cfs600 (102 cfs m(1302/s) m recorded3/s) recorded in October in October of 2006. of 2006. The The average average flow flow during during this periodthis period was 16,462was 16,462 cfs (467 cfs m(4673/s). m Figure3/s). Figure4 shows 4 shows a Skagit a Skagit River River flow hydrograph flow hydrograph from 1988 from to 1988 2010. to 2010.Using a combination of total suspended solids (TSS) grabs and turbidity measurements for fine sedimentUsing (i.e., a combination silt- and clay-sized of total suspended particles smaller solidsthan (TSS) 0.0625 grabs mm) and turbidity and fine- measurements to medium-sized for sand fine (0.0625–0.5sediment (i.e., mm), silt- USGS and clay developed-sized particles a suspended smaller sediment-rating than 0.0625 mm) curve and fine for- the to medium Mt. Vernon-sized site sand by (0.0625Curran– et0.5 al. mm) [15], asUSGS follows: developed a suspended sediment-rating curve for the Mt. Vernon site by Curran et al.S [15]= 1 as× follows10−5 ×:Q 2.32 Q < 27,400 cfs (776 m3·s−1) (4)

S = 1 × 10S −5= × 3 Q×2.3210 −13 × Q3.74Q < 27,27,400400 cfs (776 (776 m m33··ss−−11)) < Q < 66,100 cfs (1872 m3·s−1)(4) (5)

−2 1.41 3 −1 S = 3 × 10S =−134.53 × Q3.74× 10 × Q27,400 Q(776> 66,100m3·s −1)cfs < Q (1872 < 66, m100· scfs )(1872 m3·s −1) (5) (6) where S = sediment load in tons/day, and Q = Skagit River ﬂow at Mt. Vernon in cubic feet per S = 4.53 × 10−2 × Q1.41 Q > 66,100 cfs (1872 m3·s −1) (6) second (cfs). whereBased S = sediment on this 24 loadyear record,in tons/day the Skagit, and Q River = Skagit averages River a sediment flow at Mt. discharge Vernon of in nearly cubic 4feet million per secondtons/year (cfs) sediment,. at an average TSS concentration of 162 mg/L. A time series of TSS at Mt. Vernon estimatedBased using on this the 24 above year record, regressions the Skagit is also River presented averages in Figure a sediment4 for the discharge period 1988 of nearly to 2010. 4 million tons/year sediment, at an average TSS concentration of 162 mg/L. A time series of TSS at Mt. Vernon estimated using the above regressions is also presented in Figure 4 for the period 1988 to 2010.

J. Mar. Sci. Eng. 2017, 5, 19 8 of 22 J. Mar. Sci. Eng. 2017, 5, 19 8 of 22

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Figure 4. Skagit River daily ( a) average ﬂowflow and (b) estimated TSS at Mt. Vernon, Washington.Washington.

In addition to the sediment load, the USGS study by Curran et al. [15] also provided grain size In addition to the sediment load, the USGS study by Curran et al. [15] also provided grain size distribution information based on analysis of water column grab samples also collected at Mt. distribution information based on analysis of water column grab samples also collected at Mt. Vernon Vernon gage. Their results indicate that more than 50% of sediments have a grain size smaller than gage. Their results indicate that more than 50% of sediments have a grain size smaller than 0.0625 mm. 0.0625 mm. This class of sediment belongs to silt and clay class and is often transported as This class of sediment belongs to silt and clay class and is often transported as suspended or wash suspended or wash load. The remaining sediment is distributed in various grain sizes. However, load. The remaining sediment is distributed in various grain sizes. However, only about 3% of the only about 3% of the total sediments are in 0.5–1 mm range and are transported as bedload. total sediments are in 0.5–1 mm range and are transported as bedload. Based on examinations of available data on TSS in combination with bed sediment properties Based on examinations of available data on TSS in combination with bed sediment properties and and bed elevations, estimates of sediment load and channel erosion or accretion in the Skagit and bed elevations, estimates of sediment load and channel erosion or accretion in the Skagit and Padilla Padilla Bay system have been developed. USACE conducted a Flood Hazard Mitigation Study [16], Bay system have been developed. USACE conducted a Flood Hazard Mitigation Study [16], during during which considerable bed sediment information was collected. The sediment types in the forks which considerable bed sediment information was collected. The sediment types in the forks and the and the upstream reaches were primarily medium to coarse sand. The mean bed sediment diameters upstream reaches were primarily medium to coarse sand. The mean bed sediment diameters in the in the North and South Forks were 0.46 and 0.6 mm, respectively. The mean diameter in the North and South Forks were 0.46 and 0.6 mm, respectively. The mean diameter in the Cottonwood Cottonwood Island region near the confluence of North and South Forks and the upstream reach Island region near the confluence of North and South Forks and the upstream reach was reported as was reported as 0.6 mm. Examination of past surveys performed by West Consultants [17] indicates 0.6 mm. Examination of past surveys performed by West Consultants [17] indicates that a significant that a significant accretion has occurred throughout the North Fork reach below the confluence near accretion has occurred throughout the North Fork reach below the confluence near Cottonwood Island Cottonwood Island from 1975 to 1999. The average accretion rate in the North Fork reach RM 4.5 to from 1975 to 1999. The average accretion rate in the North Fork reach RM 4.5 to 8.85 was 2 cm/year. 8.85 was 2 cm/year. Average accretion rate in the South Fork reach was 1.25 cm/year. Average accretion rate in the South Fork reach was 1.25 cm/year. Very little information is available on the accretion rates in Skagit and Padilla Bay tide flats. Very little information is available on the accretion rates in Skagit and Padilla Bay tide flats. WWU established a network of 23 Surface Elevation Table (SET) sites in Padilla Bay during the WWU established a network of 23 Surface Elevation Table (SET) sites in Padilla Bay during the summer summer of 2002. Data collected from the SETs through 2006 revealed a bay-wide mean surface of 2002. Data collected from the SETs through 2006 revealed a bay-wide mean surface elevation elevation change of −0.15 ± 0.15 cm/year relative to the subsurface datum indicating sediment change of −0.15 ± 0.15 cm/year relative to the subsurface datum indicating sediment erosion and erosion and loss of sediment through most of Padilla Bay except three sites near the mouth of the loss of sediment through most of Padilla Bay except three sites near the mouth of the Swinomish Swinomish Channel where deposition of 0.13 cm/year was noted [18]. This indicates that most of the Channelsediment where delivered deposition by Skagit of 0.13River cm/year remains was within noted Skagit [18]. Bay This and indicates is not transported that most of to the Padilla sediment Bay deliveredthrough the by Swinomis Skagit Riverh Channel. remains As within part Skagit of this Bay study and, a is sediment not transported trap was to Padillaestablished Bay throughnear the mouth of Skagit River. This well-known depositional area recorded a bed elevation change of 8

J. Mar. Sci. Eng. 2017, 5, 19 9 of 22 the Swinomish Channel. As part of this study, a sediment trap was established near the mouth of Skagit River. This well-known depositional area recorded a bed elevation change of 8 cm/year based on a 15 day deployment from 18 November 2008 to 3 December 2008, during which the average river ﬂow was 12,000 cfs (340 m3/s). Coastal Geological Services conducted a sedimentation study of Swinomish Channel. Shoaling rate analysis was conducted to assess the rates and patterns in which the Swinomish Channel bed was ﬁlling up because of sediment loads from connecting water bodies and surrounding uplands [19]. Their analysis based on examination of pre-and post-dredging records showed an average bed accretion rate of 28 cm/year during the period from 2004 to 2008 in the Swinomish Channel. This value is representative of the sedimentation rate of area at the mouth and sedimentation rates at other locations in the channel were even higher. Previous estimates of sediment deposition rates in the study domain are summarized in Table2. A shoaling analysis conducted by USACE in the southern reach of the Swinomish Channel based on annual channel conditions surveys from 2008 to 2015 indicates that approximately 34,000 cubic yards (25,995 m3) per year on average are deposited in the channel that require dredging.

Table 2. Sediment accretion estimates in the Skagit River Estuary and Padilla Bay. (g.d.w. stands for gram dry weight, and s.d. stands for standard deviation).

Representative Sediment Source Description Study Results Accretion Rate Estimate cm/Year Skagit Bay and Swinomish Preliminary estimate of sediment Channel: Uniform distribution accretion rate using annual Skagit Bay study domain including and deposition of sediments in Khangaonkar et al. [20] average sediment load Swinomish Channel Skagit Bay study area of (3,962,084 tons/year based on ≈2 cm/year (1.6 × 108 m2, porosity of 0.4, average of load from 1988 to 2010) and density of 2650 kg/m3) Sediment Trap and Feldspar ﬁve Skagit Bay Marsh: marker horizons/grids at Skagit Mean accretion in sediment Skagit Bay nearshore Rybczyk, J. [21]—EPA Bay Nearshore site: trap = 5.15 g.d.w. ± 2.3 (s.d.) = Station—Accretion from the 15-day STAR Grant project N 48◦21025.100, W 122◦28033.800. 334.6 g/m2 in 15 days sample in 2008, (unpublished data) Accretion rate was noted over the Bed elevation change ≈8 cm/year markers during a 15 day period 0.33 ± 0.23 (s.d.) cm/15 days (11/18/08 to 12/3/08) Padilla Bay: Most sites in Rate of elevation change derived Padilla show erosion except the from the linear regression of Padilla Bay sediment accretion rates three below Kairis and Rybczyk [18] surface elevation changes at at selected sites 12 (b)—0.13 cm/year multiple sites in Padilla Bay from ≈0.13 cm/year 14 (b) —0.12 cm/year 2002 to 2010 8–0.16 cm/year Swinomish Channel Swinomish Channel: Swinomish channel average Coastal Geological Sedimentation Study—Shoaling Analysis of dredging and survey accretion rate based on Services [19] rate analysis using records from two periods 2004–2008 records dredging records 2001–2003 and 2004–2008 ≈28 cm/year Average accretion rate based on 24 year record, Skagit River (RM 10.1 to RM 18) USACE [22] Sediment Budget and Fluvial Skagit River, North Fork and ≈1.75 cm/year Skagit River Flood Risk Geomorphology. South Fork: N.F. Skagit River Management General Examination of Skagit River bed Comparison of surveyed cross (RM 4.5 to RM 8.85) Investigation elevation changes sections between 1975 and 1999. ≈2 cm /year S.F. Skagit River (RM 5.8 to 9.25) ≈1.25 cm/year

2.2.2. Skagit River Sediment Transport Model Setup The Skagit River Sediment Transport Model setup and validation was conducted using data collected by WHOI from 2009. The monitoring stations are shown in Figure2b (green diamond). As described in Ralston et al. [11], instrument frames for high-resolution sampling within about 1 m of the bed were deployed at ﬁve locations in the intertidal zone. Near-bed instruments included pulse-coherent acoustic Doppler proﬁlers (pcADPs), acoustic backscatter sensors (ABSs), acoustic Doppler veloci-meters (ADVs), conductivity-temperature (CT) sensors, and optical backscatter sensors J. Mar. Sci. Eng. 2017, 5, 19 10 of 22

(OBSs), as well as upward-looking acoustic Doppler current profilers (ADCPs) and pressure sensors. Surface buoys at each station had CTs and OBSs for near-surface water properties, and two of the buoys had meteorological instrument packages for wind, air temperature, and barometric pressure. Near-bottom and near-surface water bottle samples were obtained to calibrate the optical and acoustic backscatter sensors, including samples collected at the instrument frames. Water samples were filtered, dried, and weighed to determine TSS, which were correlated with shipboard and moored acoustic and optical backscatter [13]. The sediment transport model used in this study is based on the Community Sediment Transport Model of Warner et al. [23]. Its capabilities include the ability to couple with wave models, multiple sediment classes, suspended and bedload computations, bed slope, morphology, and sediment density effects. Suspended sediment transport calculations are conducted through source and sink terms through vertical settling and exchange with bed layer. Exchange with bed is conducted using erosion flux formulation of Ariathurai and Arulanandan [24]. Bed load computations are conducted using the Meyer–Muller method [25]. The model was set up using three sediment classes consisting of fine silt, silt, and fine sand based on sediment samples collected from the tide flats. Bed roughness was set uniform with “z0” of 1.5 mm and one sediment bed layer. Table3 below provides a listing of the sediment model parameters used in this application.

Table 3. Sediment properties and model input parameters.

Model Parameter Fine Silt Silt Fine Sand Settling velocity, m·s−1 0.1 1.0 10.0 Mean diameter, mm 0.014 0.04 0.14 Erosion rate, kg·m−2·s−1 1.2 × 10−5 1.2 × 10−4 1.2 × 10−3 Critical stress for erosion, N·m−2 0.05 0.08 0.15 Porosity 0.65 0.60 0.55 Fractional composition 0.15 0.45 0.40 (river load and Initial sediment bed)

SSC at the river boundary was speciﬁed using a modiﬁed version of the USGS rating curve from Curran et al. [15] of the form 1.4 Qr C = Co· (7) Qro −1 −1 3 −1 where C is the SSC (mg·L ), Co is a reference concentration (165 mg·L ), Qr is the discharge (m ·s ), 3 −1 and Qro is the mean annual discharge (470 m ·s ). This rating curve also matches the rating curve used by Ralston et al. [11].

2.3. Hydrodynamic and Sediment Model Validation Simulated hydrodynamic and sediment properties such as velocity, salinity and TSS were compared with measured data from the 2009 WHOI study [11]. ADCP data were available at stations 3c, 2f and 1c for bottom velocity comparison (Figure5). We compared the east ( u) and north (v) bottom velocity components with model results. The bottom and surface current magnitudes predicted by the model appear to match the measured data reasonably well (SS of 0.52 to 0.85). However, the model seems to underpredict the bottom velocity at station 1c. This discrepancy may be because the station is located near the edge of the tide ﬂat and model grid bathymetry may not have accurately captured the local channel depths and slopes. The effect of wetting and drying on tidal ﬂats are included in the model simulation. This creates higher velocity in the tidal channels as they drain, but zero velocity when dry. This is seen in the time series at stations 3c and 2f, which show higher velocities and gaps indicating periods during which the associated cells became dry. J. Mar. Sci. Eng. 2017, 5, 19 11 of 22 predicted by the model appear to match the measured data reasonably well (SS of 0.52 to 0.85). However, the model seems to underpredict the bottom velocity at station 1c. This discrepancy may be because the station is located near the edge of the tide flat and model grid bathymetry may not have accurately captured the local channel depths and slopes. The effect of wetting and drying on tidal flats are included in the model simulation. This creates higher velocity in the tidal channels as theyJ. Mar. drain Sci. Eng., but2017 zero, 5, 19 velocity when dry. This is seen in the time series at stations 3c and 2f, which11 of 22 show higher velocities and gaps indicating periods during which the associated cells became dry.

Figure 5. ComparisonComparison of of bottom bottom currents currents in in Skagit Skagit tidal tidal flatsﬂats shown at stations 3c, 2c, 2f and 1c during June of 2009 asas partpart ofof sedimentsediment modelmodel setupsetup andand calibration.calibration. ((uuobsobs = observed east velocity component, vobsobs == observed observed north north velocity component, umodmod == modeled modeled east east velocity velocity component and vmodmod == modeled modeled north north velocity velocity component) component)..

Figure 6 shows the time series comparison of bottom stress at stations 2c, 2f and 3c. The model Figure6 shows the time series comparison of bottom stress at stations 2c, 2f and 3c. The model reasonably captures periodic peaks of bottom stress during peak ebb and low tidal conditions. The reasonably captures periodic peaks of bottom stress during peak ebb and low tidal conditions. model underpredicts bottom stress at low tide for station 2c but it performs quite well for stations 3c The model underpredicts bottom stress at low tide for station 2c but it performs quite well for stations and 2f. During this period, bottom velocity peak at 0.5 m/s creates high bottom stress and conditions 3c and 2f. During this period, bottom velocity peak at 0.5 m/s creates high bottom stress and conditions suitable for high seabed erosion. These results indicate that accurate description of local bathymetry suitable for high seabed erosion. These results indicate that accurate description of local bathymetry in in an environment undergoing morphological change is important for accurate model predictions. an environment undergoing morphological change is important for accurate model predictions. Examination of bottom shear stress was of major importance in the validation process due to its Examination of bottom shear stress was of major importance in the validation process due to its direct influence on sediment erosion and deposition process and corresponding measurable direct influence on sediment erosion and deposition process and corresponding measurable response response in TSS concentration. The bed shear stress is calculated within FVCOM at each time step in TSS concentration. The bed shear stress is calculated within FVCOM at each time step from the from the instantaneous bottom layer flow velocity using a logarithmic profile representation of the instantaneous bottom layer flow velocity using a logarithmic profile representation of the boundary boundary layer. The formulation of bed shear stress is as follows: layer. The formulation of bed shear stress is as follows: 2 τ푏 = ρ퐶푑|푢∗| (8) 2 τb = ρCd|u∗| (8) where ρ is sea water density, Cd is the bottom drag coefficient and |푢∗| is the critical shear velocity, which is related to bed roughness. where ρ is sea water density, Cd is the bottom drag coefficient and |u∗| is the critical shear velocity, whichFigure is related 7 shows to bed the roughness. comparison of observed TSS in Skagit Bay tide flats at stations 3c and 1c. The high Figurebottom7 stressshows during the comparison peak ebb current of observed periods TSS over in Skagitthe tide Bay flats tide results flats in at significant stations 3c increase and 1c. Theof bed high shear bottom and stresscorresponding during peak increase ebb current in TSS, periods varying over from the 200 tide to flats 400 resultsmg/L for in significantstations 3c increase and 1c, respectivelyof bed shear, andas shown corresponding in Figure increase 7. Also in shown TSS, varying in the from plot 200are to variations 400 mg/L of for bottom stations and 3c surface and 1c, salinityrespectively, influenced as shown by ina Figurecombination7. Also of shown tidal incirculation the plot are and variations river plume. of bottom The andstrong surface response salinity of influenced by a combination of tidal circulation and river plume. The strong response of salinity due to freshwater plume can be seen at station 3c. The bottom salinity can be as low as 5 ppt during low tidal periods. Further offshore, station 1c shows that the influence of freshwater plume is weaker and higher salinities are noted. J. Mar. Sci. Eng. 2017, 5, 19 12 of 22 salinity due to freshwater plume can be seen at station 3c. The bottom salinity can be as low as 5 ppt during low tidal periods. Further offshore, station 1c shows that the influence of freshwater plume is duringJ. Mar. Sci. low Eng. tidal2017 ,period5, 19 s. Further offshore, station 1c shows that the influence of freshwater plume12 of 22is weaker and higher salinities are noted.

FFigureigure 6.6. Comparison of observed bottom stress in Skagit tidal flats ﬂats shown at stati stationsons 3c, 2c and 2f obs during June of 20092009 asas partpart ofof sedimentsediment modelmodel setupsetup andand calibration.calibration. ((ττobsobs = observed bottom shear mod stress and τmodmod == modeled modeled bottom bottom shear shear stress) stress)..

obsobs obsobs Figure 7. 7. ComparisonComparison ofof observedobserved salinitysalinity ((ssobs-bot-bot == observed bottombottom salinity,salinity, ssobs-suf-suf == observed modmod modmod bottom salinity, ssmod--botbot = modeled modeled bottom salinity and ssmod--sufsuf = = modeled modeled surface surface salinity) salinity) and SSC obsobs obsobs (sscobs--absabs = = observed observed acoustic acoustic backscatter backscatter sensor suspended sediment,sediment, sscsscobs--advadv = observed observed acoustic modmod Doppler velocitymeter velocitymeter suspended suspended sediment sediment and andssc sscmo=d modeled= modeled suspended suspended sediment) sediment) in Skagit in Skagit tidal tidalﬂats atflats stations at stations 3c and 3c 1c. and 1c.

J. Mar. Sci. Eng. 2017, 5, 19 13 of 22

J. Mar. Sci. Eng. 2017, 5, 19 13 of 22 2.4. Application to Dike Repair and Restoration Scenarios 2.4. Application to Dike Repair and Restoration Scenarios We conducted two sensitivity tests using the model to examine hypothetical scenarios involving We conducted two sensitivity tests using the model to examine hypothetical scenarios modifications to the existing jetties and dikes near the mouth of north fork of Skagit River and involving modifications to the existing jetties and dikes near the mouth of north fork of Skagit River compared the hydrodynamics and sediment transport response to baseline (existing conditions). and compared the hydrodynamics and sediment transport response to baseline (existing A 20 day (10 June 2009 to 30 June 2009) simulation of hydrodynamics and sediment transport was conditions). A 20 day (10 June 2009 to 30 June 2009) simulation of hydrodynamics and sediment conducted for baseline, and two scenarios with dike modification during the WHOI field data collection transport was conducted for baseline, and two scenarios with dike modification during the WHOI period.field data The predictionscollection period. of time The averaged predictions salinity, of time bottom averaged shear salinity, stress, and bottom TSS distributionsshear stress, and simulated TSS neardistrib McGlinnutions and simulated Goat Island near locations McGlinn of and interest Goat for Island the respective locations of scenarios interest were for the compared respective with thescenarios baseline were condition compared as part with of thisthe assessment.baseline condition A close-up as part of of the this baseline assessment. grid is A shown close-up in Figureof the 8 alongbaseline with grid bathymetry is shown used in Figure in baseline 8 along scenario with bathymetry developed used using in baseli bathymetricne scenario information developed from using the 2014bathymetric channel and information Lidar surveys. from the 2014 channel and Lidar surveys.

Figure 8. Close-up of the model grid and bathymetry used in baseline (or existing conditions) Figure 8. Close-up of the model grid and bathymetry used in baseline (or existing conditions) simulation. Note—color contours indicate depths (negative elevations) relative to NAVD88 datum. simulation. Note—color contours indicate depths (negative elevations) relative to NAVD88 datum. We then modified the baseline grid to generate the following two scenarios of interest shown in FigureWe then 9: modified the baseline grid to generate the following two scenarios of interest shown in Figure9:  SCN-1, South Jetty Repair: Recent surveys by USACE indicate that South Jetty of the Swinomish • SCN-1,Channel South (see Jetty Figure Repair: 1, C l Recentocation) surveys that extends by USACE southwest indicate from that Goat South Island Jetty along of thethe Swinomishsouthern Channelbank of (see the Swinomish Figure1, C Channel location) has that structurally extends southwest degraded (jetty from elevations Goat Island reduced along from the southern ≈1.9 m bankto as of low the Swinomishas −1.1 m), allowing Channel leakage has structurally flow and degradedtransport from (jetty adjacent elevations flats reduced to the Swinomish from ≈1.9 m toChannel. as low as In− 1.1 SCN m),-1, allowing the South leakage Jetty is flow repaired and transport by re-setting from the adjacent elevations flats of to the the dike Swinomish crest Channel.nodes back In SCN-1, to 1.9 m the (NAVD88) South Jetty, thereby is repaired restoring by re-setting the functionality the elevations of the South of the Jetty dike. The crest main nodes backobjective to 1.9 mof (NAVD88),this scenario thereby is to evaluate restoring if this the repair functionality would res ofult the in South improvement Jetty. The (reduction) main objective in ofsediment this scenario transport is to evaluateinto the Swinomish if this repair Channel. would resultSCN-1 inSouth improvement Jetty Repair (reduction) location is inshown sediment in transportFigure 9a into. the Swinomish Channel. SCN-1 South Jetty Repair location is shown in Figure9a.  SCN-2, McGlinn Causeway Restoration: This habitat restoration proposal involves breaching of • SCN-2, McGlinn Causeway Restoration: This habitat restoration proposal involves breaching of the causeway between McGlinn Island and mainland (see Figure 1, D location) and reduction of the causeway between McGlinn Island and mainland (see Figure1, D location) and reduction of the crest elevations of the north section of the McGlinn Island to Goat Island Jetty (see Figure the crest elevations of the north section of the McGlinn Island to Goat Island Jetty (see Figure2b). 2b). The restoration design calls for reduction in the crest elevation (from ≈3.0 m) to 1.33 m ≈ The(NAVD88) restoration corresponding design calls forto mean reduction sea level in the (MSL crest = elevation 0) at the (fromnorth section3.0 m) of to the 1.33 Goat m (NAVD88) Island correspondingjetty allowing to amean direct sea connection level (MSL between= 0) at the the north North section Fork of of the the Goat Skagit Island River jetty allowingand the a directSwinomish connection Channel between during the high North tides. Fork The of causeway the Skagit breach River andwas theincorporated Swinomish by Channel reducing during the highelevation tides. of The 2.5 causewaym of the causeway breach wasto an incorporated elevation of −0.3 by m reducing (NAVD88) the. In elevation additionof to 2.5providing m of the causewaybetter connectivity to an elevation and of restoring−0.3 m (NAVD88). historic pathways In addition for to upstre providingam and better downstream connectivity fish and restoringmigration, historic the objective pathways of for this upstream scenario and is to downstream examine the fish potential migration, benefits the in objective the form of of this scenarioreduction is to in examine salinity the and potential improved benefits brackish in the water form habitat.of reduction SCN- in2 salinityMcGlinn and Causeway improved brackishRestoration water locations habitat., SCN-2consisting McGlinn of causeway Causeway breach Restoration and reduction locations, of the consistingJetty crest el ofevations causeway, breachare shown and reduction in Figure of9b. the Jetty crest elevations, are shown in Figure9b.

J. Mar. Sci. Eng. 2017, 5, 19 14 of 22

J. Mar. Sci. Eng. 2017, 5, 19 14 of 22 Also of interest are potential impacts that each scenario may impose on the overall estuarine Also of interest are potential impacts that each scenario may impose on the overall estuarine functionsfunctions and and on on their their respective respective beneficial beneficial objectives.objectives. For For example, example, the the existing existing condition condition with with the the breachbreach in in the the Swinomish Swinomish Channel Channel SouthSouth JettyJetty likely results in in some some improvement improvement to toconnectivity connectivity andand brackish brackish water water benefits benefits and and itsits repairrepair maymay eliminate the the access access and and affect affect salinity salinity levels levels along along thethe channel. channel. Similarly, Similarly, McGlinn McGlinn Causeway Causeway restorationrestoration ac actionstions while while conveying conveying habitat habitat restoration restoration benefitsbenefits may may impact/increase impact/increase sediment sediment transport transport or or deposition deposition inin thethe SwinomishSwinomish Channel,Channel, resulting in increasedin increased dredging dredging and maintenance. and maintenance. The sensitivity The sensitivity analysis analysis presented presented below below using using identical identical forcing andforcing sediment and loading sediment conditions loading conditionsallows an assessment allows an assessment of relative merits of relative and impacts merits and to beneficial impacts touses ofbeneficial both scenarios. uses of both scenarios.

(a) (b)

Figure 9. Modified model configuration used for (a) SCN-1 South Jetty Repair and (b) SCN-2, Figure 9. Modified model configuration used for (a) SCN-1 South Jetty Repair and (b) SCN-2, McGlinn Causeway Restoration. Note—color contours indicate depths (negative elevations) relative McGlinn Causeway Restoration. Note—color contours indicate depths (negative elevations) relative to to NAVD88 datum. NAVD88 datum. 3. Results 3. Results A qualitative assessment of the sensitivity of sediment transport and salinity to the proposed restorationA qualitative and repair assessment scenarios of is the presented sensitivity below. of sediment transport and salinity to the proposed restoration and repair scenarios is presented below. 3.1. Assessment of Jetty Repair Scenario, SCN-1 3.1. Assessment of Jetty Repair Scenario, SCN-1 In SCN-1 with the Jetty repairs in place, salinity distribution appears to show only small nearfieldIn SCN-1 effects with near the the Jetty repaired repairs Jetty in(see place, Figure salinity 10) due distributionto blockage of appears transport to south show of onlythe Jetty. small nearfieldThe magnitude effects near of freshwater the repaired transported Jetty (see Figure through 10 the) due gap to blockagein the degraded of transport portion south of jetty of the was Jetty. Therelatively magnitude small offreshwater and does transported not appear through to cause the noticeable gap in the impacts degraded toportion salinity of gradients jetty was relatively in the smallSwinomish and does Channel not appear at the to plotted cause noticeablescale of 0 to impacts 32 ppt. toA difference salinity gradients-plot was in added the Swinomish at the end of Channel this at thesection plotted to highlight scale of 0 theto 32 relative ppt. A differencesdifference-plot in time was added averaged at the concentrations. end of this section Small to increases highlight in the relativesalinity differences between McGlinn in time averaged and Goat concentrations. Island and small Small decreases increases in salinity in salinity at the between southern McGlinn part of and GoatJetty Island Island and are small noticeable decreases. in salinity at the southern part of Jetty Island are noticeable. BottomBottom shear shear stress stress also also shows shows locallocal effectseffects mostly near near the the Goat Goat Island Island region region (see (see Figure Figure 11). 11 ). RepairingRepairing the the jetty jetty creates creates slightly slightly higherhigher velocitiesvelocities and bottom bottom shear shear stress stress along along the the Swinomish Swinomish Channel.Channel. In In baseline baseline simulation, simulation, bottom shear shear stress stress is is noticeably noticeably higher higher in in the the jetty jetty gap gap region. region. Interestingly,Interestingly, higher higher bottom bottom shear shear stress stress isis noticeablenoticeable over the the tidal tidal flat flat just just north north of of the the Swinomish Swinomish Channel North Jetty. Repaired jetty confines the tidal flow to the Swinomish Channel and prevents Channel North Jetty. Repaired jetty confines the tidal flow to the Swinomish Channel and prevents exchange to the south to Skagit Bay tidal flats via the breach. This likely increases the velocities and exchange to the south to Skagit Bay tidal flats via the breach. This likely increases the velocities and exchange over the north side tidal flats and therefore results in slightly higher bed shear. exchange over the north side tidal flats and therefore results in slightly higher bed shear. Repairing the jetty decreases total suspended sediment transported into the Swinomish Repairing the jetty decreases total suspended sediment transported into the Swinomish Channel. Channel. However, the volume and sediment fluxes affected by the jetty repair are relatively small However,and beneficial the volume effects and of sediment preventing fluxes a large affected volume by the of jetty TSS repair into the are Swinomish relatively small Channel and arebeneficial not effectsnoticeable of preventing in the time a large averaged volume contour of TSS plots into as the shown Swinomish in Figure Channel 12. are not noticeable in the time averaged contour plots as shown in Figure 12.

J. Mar. Sci. Eng. 2017, 5, 19 15 of 22 J. Mar.J. Mar. Sci. Sci. Eng. Eng. 2017 2017, 5, ,5 19, 19 1515 of of 22 22 J. Mar. Sci. Eng. 2017, 5, 19 15 of 22

(a) (b) (a) (b) Figure 10. Time averaged(a) salinity distribution (20 days) for (a) baseline conditions(b) and (b) Jetty FigureFigure 10. 10.Time Time averaged averaged salinity salinity distribution distribution (20 (20 days) days) for (fora) baseline (a) baseline conditions conditions and and(b) Jetty (b) Jetty Repair FigureRepair 10. Scenario, Time averagedSCN-1. salinity distribution (20 days) for (a) baseline conditions and (b) Jetty Scenario,Repair Scenario, SCN-1. SCN-1. Repair Scenario, SCN-1.

(a) (b)

(a) (b) Figure 11. Time averaged(a) bottom shear stress distribution (20 days) for (a) (baselineb) conditions and Figure(b) Jetty 11. Rep Timeair averagedScenario, SCNbottom-1. shear stress distribution (20 days) for (a) baseline conditions and FigureFigure 11. 11.Time Time averaged averaged bottom bottom shearshear stressstress distributiondistribution (20 (20 days) days) for for (a (a) )baseline baseline conditions conditions and and (b) Jetty Repair Scenario, SCN-1. (b)(b Jetty) Jetty Repair Repair Scenario, Scenario, SCN-1. SCN-1.

(a) (b)

Figure 12. Time averaged(a) total suspended sediment (TSS) distribution (20(b days)) for (a) baseline conditions and (b) Jetty(a )Repair Scenario, SCN-1. (b) Figure 12. Time averaged total suspended sediment (TSS) distribution (20 days) for (a) baseline Figure 12. Time averaged total suspended sediment (TSS) distribution (20 days) for (a) baseline FigureconditionsThe 12. differenceTime and ( averagedb plot) Jetty at Repairthe total end Scenario, suspendedof this section SCN sediment-1 . shows the (TSS) difference distribution between (20 baseline days) for conditions (a) baseline and conditions and (b) Jetty Repair Scenario, SCN-1. SCNconditions-1 for shear and stress (b) Jetty and Repair TSS. Scenario, SCN-1. The difference plot at the end of this section shows the difference between baseline conditions and The difference plot at the end of this section shows the difference between baseline conditions and SCN -1 for shear stress and TSS. SCNThe-1 for difference shear stress plot and at theTSS. end of this section shows the difference between baseline conditions and SCN-1 for shear stress and TSS.

J. Mar. Sci. Eng. 2017, 5, 19 16 of 22 J. Mar. Sci. Eng. 2017, 5, 19 16 of 22 J. Mar. Sci. Eng. 2017, 5, 19 16 of 22 3.2. Assessment of McGlinn Causeway Restoration Scenario, SCN-2 3.2. Assessment of McGlinn Causeway Restoration Scenario, SCN-2 3.2. AssessmentThe SCN- 2of scenarioMcGlinn withCauseway breaching Restoration of the Scenario, causeway SCN and-2 reduction in crest elevation of the The SCN-2 scenario with breaching of the causeway and reduction in crest elevation of the north northThe section SCN of-2 the scenario Goat Island with breachingjetty results of in the large causeway freshwater and volume reduction fluxes in crestfrom elevationthe Skagit of River the section of the Goat Island jetty results in large freshwater volume fluxes from the Skagit River into northinto the section Swinomish of the GoatChannel. Island As jetty shown results in Figure in large 13, freshwater there is a volumedramatic fluxes reduction from inthe salinity Skagit levelsRiver the Swinomish Channel. As shown in Figure 13, there is a dramatic reduction in salinity levels in intoin the the Swinomish Swinomish Channel Channel. and As the shown influence in Figure extends 13, fromthere Goatis a dramatic Island all reduction the way upin salinitynorth into levels the the Swinomish Channel and the influence extends from Goat Island all the way up north into the inSwinomish the Swinomish Channel Channel towards and Padilla the influence Bay. Difference extends fromplot at Goat the Islandend of allthe the section way upshows north salinity into the in SwinomishSwinomishSCN-2 can Channel be Channel up to towards20 towards ppt lower PadillaPadilla than Bay. Bay.baseline DifferenceDifference. While salinityplot plot at at the thereduction end end of of theis the dominant section section shows during shows salinity ebb salinitys, the in in SCN-2SCNcauseway- can2 can be be breach up up to to 20 continues20 ppt ppt lower lower to than than push baseline.baseline freshwater. While into salinity salinity the Swinomish reduction reduction is ischannel dominant dominant during during during flood ebb ebbs,s , tidethe the causewaycausewayperiods. breach breach continues continues to push to push freshwater freshwater into into the Swinomishthe Swinomish channel channel during during flood flood tide periods. tide periods.

(a) (b) Figure 13. Time averaged(a) salinity distribution (20 days) for (a) baseline conditions(b) and (b) McGlinn Figure 13. Time averaged salinity distribution (20 days) for (a) baseline conditions and (b) McGlinn Causeway restoration, SCN-2. CausewayFigure 13 restoration,. Time averaged SCN-2. salinity distribution (20 days) for (a) baseline conditions and (b) McGlinn Causeway restoration, SCN-2. Significant changes to bed shear stress are noted for SCN-2 as shown in Figures 14. High bottom shearSignificantSignificant stress is changesfound changes near to to bed bedthe shearlocationsshear stressstress of areJetty noted and forCauseway for SCN SCN-2-2 as modifications. as sh shownown in inFigure Figure Thes 14lowering 14. High. High bottom of bottom the shearshearJetty stress and stress Causeway is foundis found near crest near the elevations the locations locations results of Jettyof Jettyin andtransport and Causeway Causeway of the modifications.Skagit modifications. River water The The over lowering lowering the structures of of the the Jetty andJettydirectly Causeway and into Causeway crestthe Swinomish elevations crest elevations Channel results results in at transport the in two transport oflocations. the Skagitof th Thise Skagit River results waterRiver in highwater over velocities the over structures the structuresbed shear directly intodirectlyrelative the Swinomish into to baseline the Swinomish Channel at the locations atChannel the two withat locations.the modifications. two locations. This results Interestingly, This inresults high in significant velocities high velocities bed decrease shear bed in shear relative bed torelative baselineshear stress to at baseline theis noted locations at a the tidal with locations flat modifications. between with the modifications. Goat Interestingly, Island Interestingly,Jetty significant and the South significant decrease Jetty of in decrease the bed Swinomish shear in bed stress is notedshearChannel. stress at aFurthermore tidal is noted flat at between ,a some tidal flatincrease the between Goat of Island bottom the Goat Jetty shear Island and stress theJetty is South andnoted the Jetty near South ofthe theJetty existing Swinomish of the breach Swinomish Channel. of the Furthermore,Channel.South Jetty Furthermore someat Goat increase Island, some ofbecause increase bottom of shearofmodified bottom stress tidalshear is noted flow stress and near is notedcir theculation existing near thein breach thisexisting scenario. of breach the SouthNote of ,the Jettyin atSouth GoatSCN-2, IslandJetty the breachat because Goat is Island retained of modified because as in baseline tidalof modified flow conditions and tidal circulation flow without and repairs.cir inculation this scenario. in this Note,scenario. in SCN-2,Note, in the breachSCN- is2, retainedthe breach as is in retained baseline as conditions in baseline without conditions repairs. without repairs.

(a) (b)

Figure 14. Time averaged(a) bottom shear stress distribution (20 days) for (a()b baseline) conditions and (b) McGlinn Causeway restoration, SCN-2. FigureFigure 14. 14.Time Time averaged averaged bottom bottom shearshear stressstress distribution (20 (20 days) days) for for (a ()a )baseline baseline conditions conditions and and (b) McGlinn Causeway restoration, SCN-2. (b) McGlinn Causeway restoration, SCN-2.

J. Mar.J. Mar. Sci. Sci. Eng. Eng.2017 2017, 5,, 5 19, 19 17 17of 22 of 22 J. Mar. Sci. Eng. 2017, 5, 19 17 of 22 Figure 15 shows that there is a significant increase in TSS concentration in the Swinomish ChannelFigureFigure north15 shows 15 of showsGoat that Island. there that there is a significant is a significant increase increase in TSS in concentrationTSS concentration in the in Swinomish the Swinomish Channel northChannel ofFigure Goat north Island. 16 is of a Goat difference Island.- plot showing the time averaged horizontal distribution difference betweenFigureFigure baseline16 is 16 a difference-plot isconditions a difference and- showingplot SC N showing-1 for the (a) time the salinity averaged time averaged(c) shear horizontal stress horizontal distributionand (e) distribution TSS. differenceIn this difference area between, TSS baselineconcentrationbetween conditions baseline may and increaseconditions SCN-1 by for and more (a) SC salinity thaN-1n for 500 (c)(a) mg shearsalinity as shown stress (c) shear and in Figure (e)stress TSS. 16fand In. In(e) this contrast,TSS area,. In TSSthis a reduction concentrationarea, TSS in concentration may increase by more than 500 mg as shown in Figure 16f. In contrast, a reduction in mayTSS increase concentration by more is than found 500 on mg the as shown Skagit in Bay Figure side 16 southf. In contrast, of Goat Island a reduction Jetty. in This TSS impli concentrationes that TSS concentration is found on the Skagit Bay side south of Goat Island Jetty. This implies that significant TSS from North Fork Skagit River was transported via modified sections into the is foundsignificant on the SkagitTSS from Bay North side south Fork of Skagit Goat River Island was Jetty. transported This implies via that modified significant sections TSS into from the North Swinomish Channel. ForkSwinomish Skagit River Channel was transported. via modified sections into the Swinomish Channel.

(a()a ) (b(b) ) Figure 15. Time averaged total suspended sediment (TSS) distribution (20 days) for (a) baseline FigureFigure 15. 15.Time Time averaged averaged total total suspended suspended sediment (TSS) (TSS) distribution distribution (20 (20 days) days) for for (a) ( a baseline) baseline conditions and (b) McGlinn Causeway restoration, SCN-2. conditionsconditions and and (b ()b McGlinn) McGlinn Causeway Causeway restoration,restoration, SCN-2.SCN-2.

(a) (b) (a) (b)

Figure 16. Cont. J. Mar. Sci. Eng. 2017, 5, 19 18 of 22 J. Mar. Sci. Eng. 2017, 5, 19 18 of 22

(e) (f)

Figure 16. Time averaged horizontal distribution difference between baseline conditions and SCN-1 Figure 16. Time averaged horizontal distribution difference between baseline conditions and SCN-1 for (a) salinity (c) shear stress and (e) TSS; time averaged horizontal distribution difference between for (a) salinity (c) shear stress and (e) TSS; time averaged horizontal distribution difference between baseline conditions and SCN-2 for (b) salinity (d) shear stress and (f) TSS. The positive sign of the baseline conditions and SCN-2 for (b) salinity (d) shear stress and (f) TSS. The positive sign of the color color bar means that the baseline concentrations are higher than the selected scenario. bar means that the baseline concentrations are higher than the selected scenario. 4. Discussion 4. Discussion To facilitate quantitative comparison of scenarios, we selected two stations near the proposed projectTo facilitate sites in quantitativethe Swinomish comparison Channel. Station of scenarios, A was weselected selected near two the stationsSouth Jetty near breach the proposed-repair projectlocation sites near in Goat the Swinomish Island. It is Channel.the region Stationwhere high A was TSS selected was predicted near the in SCN South-2 Jettyand is breach-repair marked in locationFigure near2b (red Goat circles). Island. We It also is the selected region another where station high TSS, station was B, predicted at the mouth in SCN-2 of north and section is marked of the in FigureSwinomish2b (red Channel circles). Wewhere also high selected salinity another fluctuation station, was station noted B,in atSCN the-2 mouth simulations. of north section of the SwinomishQuantitative Channel comparisons where high of salinity simulated fluctuation hydrodynamic was noted parameters in SCN-2 are simulations. shown in Figure 17 for baseline,Quantitative SCN-1, comparisonsand SCN-2 scenarios of simulated at these hydrodynamic two stations. The parameters percentage are differen shownce in between Figure 17the for baseline,two scenarios SCN-1, relative and SCN-2 to baseline scenarios conditions at these for two salinity, stations. shear The stress percentage and TSS are difference shown in between Table 4 the. twoNegative scenarios percentage relative toimplies baseline that conditionsthe magnitude for salinity,of the simulated shear stress variable and TSSin the are scenario shown is in lower Table 4. Negativethan the percentage baseline. On implies the otherthat the hand, magnitude positive of percentage the simulated implies variable that the in the magnitude scenario of is lower the thansimulated the baseline. variable Ons theis higher other compare hand, positived to the percentage baseline result. implies that the magnitude of the simulated variablesFigure is higher 17 shows compared that the to proposed the baseline project result. scenarios do not have a significant effect on water surface elevations. Plots of water surface elevations at both sites are nearly identical for baseline Figure 17 shows that the proposed project scenarios do not have a significant effect on water conditions as well as the two project scenarios. surface elevations. Plots of water surface elevations at both sites are nearly identical for baseline Because of jetty repairs in SCN-1, the time series plots of simulated variables shown in Figure conditions as well as the two project scenarios. 17a (blue lines) respond and deviate a little from the existing conditions (black lines). Eliminating the Because of jetty repairs in SCN-1, the time series plots of simulated variables shown in Figure 17a leakage of brackish water flow into the Swinomish results in small increase in salinity (7%, 3%). (blueHowever, lines) respondthe effect andon velocities deviate aand little therefore from the shear existing stress conditionsin the Swinomish (black Channel lines). Eliminatingwas minimal the leakage(−0.2%, of −0.1 brackish %). Correspondingly, water flow into near the- Swinomishbed or bottom results TSS in response small increase (−2% and in − salinity3%) and (7%, depth 3%). However,averaged the TSS effect (−5%) on was velocities also small and but therefore consistent shear with stress the in expectation the Swinomish that the Channel Jetty repairs was minimal will (−result0.2%, in− 0.1reduction %). Correspondingly, of TSS, and, therefore near-bed, reduced or bottom sediment TSS deposition response in (− the2% Swinomish and −3%) Channel. and depth averagedThese results TSS (indicate−5%) was that also the Jetty small repair but consistentscenario SCN1 with would the expectation result in relatively that the small Jetty changes repairs in will resultsalinity in reduction and TSS in of the TSS, Swinomish and, therefore, Channel reduced relative sedimentto baseline deposition conditions. in the Swinomish Channel. These resultsIn contrast, indicate as shown that the in JettyFigure repair 17b scenario(red lines), SCN-1 all variables would resultshowed in relativelya strong response small changes to the in salinityMcGlinn and Causeway TSS in the SwinomishRestoration Channel scenario relative SCN-2 as to baselineimplemented conditions. in this model sensitivity test. McGlinnIn contrast, Causeway as shown breach inand Figure Goat Island17b (red Jetty lines), crest elevation all variables reduction showed results a strong in an immediate response to thereduction McGlinn in Causeway salinity through Restoration dilution scenario by large SCN-2 volume as fluxes implemented of Skagit River in this freshwater model sensitivity that enters test. McGlinnthe Swinomish Causeway Channel breach directly. and Goat The Island salinity Jetty in crest the Swinomish elevation reduction Channel at results stations in anA andimmediate B is reductionreduced in significantly salinity through (−44% dilution and −81% by) large from volume typical fluxes values of of Skagit ≈20 ppt River to freshwater<5 ppt. This that low enters-level the Swinomishsalinity environment Channel directly. (<15 ppt) The are salinity very suitable in the Swinomishfor fish migratory Channel pathways at stations in estuaries A and B is[3, reduced26,27] significantlyand can increase (−44% fish and return−81%) rate from into typicalSkagit River. values For of example,≈20 ppt Greene to <5 ppt. et al. This [28]low-level suggested salinity that environmentfreshwater and (<15 nearshore ppt) are veryenvironmental suitable forconditions fish migratory are the main pathways controlling in estuaries factors [of3, 26the,27 survival] and can rate of Skagit River Chinook salmon. increase fish return rate into Skagit River. For example, Greene et al. [28] suggested that freshwater

J. Mar. Sci. Eng. 2017, 5, 19 19 of 22

andJ. Mar. nearshore Sci. Eng. 2017 environmental, 5, 19 conditions are the main controlling factors of the survival rate of Skagit19 of 22 River Chinook salmon. Bed shear stress stress in increasedcreased in in this this scenario scenario but but was was generally generally <5% <5% and and results results in inan anincreas increasee of ofbottom bottom TSS TSS varying varying from from an anincrease increase of of6% 6% near near station station A to A toa high a high value value of of37% 37% at atstation station B. B.It Itappears appears that that this this increase increase in in depth depth averaged averaged water water column column TSS TSS (11% (11% and and 87%) 87%) is is mos mostlytly due to suspended sedimentsediment loadload from from the the North North Fork Fork of of Skagit Skagit River River that that is transported is transported through through the Jettythe Jetty and theand Causewaythe Causeway openings openings created created in SCN-2 in SCN during-2 during ebbs. ebb Upons. Upon entering entering the Swinomishthe Swinomish Channel, Channel, the suspendedthe suspended sediments sediments are mostly are mostly transported transported to north to ofnort theh Swinomish of the Swinomish Channel. Channel. Net tidally Net averaged tidally transportaveraged throughtransport the through Swinomish the Swinomish Channel is Channel to the north is to towardsthe north Padilla towards Bay. Padilla Bay.

(a) (b)

Figure 17.17. ComparisonComparison of of time time series series of of salinity, salinity, bed bed shear shear stress stress and TSSand atTSS (a) at station (a) station A and A (b )and station (b) Bstation (Figure B 2(Figureb) for baseline, 2b) for baseline, Jetty Repair Jetty Scenario, Repair Scenario, SCN-1, and SCN McGlinn-1, and McGlinn Causeway Causeway restoration, restoration, SCN-2. SCN-2. Table 4. Percentage difference of two scenarios with the baseline for salinity, shear stress and TSS at Table 4. Percentage difference of two scenarios with the baseline for salinity, shear stress and TSS at two mooring stations. two mooring stations.

Salinity Shear Shear Stress Bottom Bottom TSSTSS TSSTSS MooringMooring SCN-1SCN-1 SCN-2SCN-2 SCN SCN-1-1 SCN SCN-2-2 SCN SCN-1-1 SCN SCN-2-2 SCN-1SCN-1 SCN-2SCN-2 AA 77 −−4444 −0.20.2 2 2 −−22 6 −5−5 1111 − − − − BB 33 −8181 −0.10.1 4 4 −33 37 5−5 8383 Bottom TSS corresponds to TSS concentration in the lower 3% of water column. Bottom TSS corresponds to TSS concentration in the lower 3% of water column.

5. Conclusions In this study, thethe FVCOMFVCOM hydrodynamichydrodynamic modelmodel waswas usedused toto examineexamine the sensitivity of estuarine conditions to selected modifications modifications of of the the structures near near the the mouth of North Fork of Skagit River estuary. Repairing the existing structures for reduction of sedimentationsedimentation and dredging may conflictconflict with interestsinterests related to creation creation of of migration migration pathways pathways and brackish brackish water habitat desirable for restoration of salmon populations through restoration of natural tidal functions.functions. A modelingmodeling based sensitivity analysis allows a relative and quantitative comparisoncomparison of potential estuarine response and effectiveness of of repair repair on on channel channel maintenance maintenance to to allow allow for for a acomprehensive comprehensive evaluation evaluation of ofimpact impact or orbenefit. benefit. A hydrodynamic model capable of resolving nearshore structures such as dikes and jetties was implemented for the Skagit River estuary. The model was validated using oceanographic data collected in 2006 and 2009. In addition to water surface elevation, velocities, and salinities, the data also included bed shear stress and TSS measurements. The baseline condition corresponding to calibration period was then used to evaluate the system response to two scenarios (1) Jetty Repair

J. Mar. Sci. Eng. 2017, 5, 19 20 of 22

A hydrodynamic model capable of resolving nearshore structures such as dikes and jetties was implemented for the Skagit River estuary. The model was validated using oceanographic data collected in 2006 and 2009. In addition to water surface elevation, velocities, and salinities, the data also included bed shear stress and TSS measurements. The baseline condition corresponding to calibration period was then used to evaluate the system response to two scenarios (1) Jetty Repair Scenario, SCN-1 and (2) McGlinn Causeway restoration, SCN-2. SCN-1 prevents leakage of flow and TSS into the Swinomish Channel, while SCN-2 provides direct migration pathways and improved conveyance of freshwater into the Swinomish Channel. The results of sensitivity tests show that SCN-1 successfully eliminated the leakage flow and transport of Skagit Bay waters into the Swinomish Channel. However, it turned out that associated volume fluxes were relatively small and beneficial effects (reduction in TSS) as well as potential negative effects (increase in salinity) from fish habitat goals were small. In other words, the estuary and Swinomish Channel response to SCN-1 was not strong. In contrast, SCN-2 was very effective in providing a direct connection (direct migration pathway) and increased freshwater transport into the Swinomish Channel. The peak reduction in salinity by almost 81% and continued northward transport are also very positive responses towards fish habitat restoration goals. However, the restoration design (Jetty crest and Causeway Breach invert elevations and lengths) is such that it allows significant Skagit River sediments to be carried into the Swinomish Channel in suspension. Given that increase in bed shear stress associated with SCN-2 is <4%, an increase in TSS of 11%–83% could result in impacting sediment deposition in the Swinomish Channel. Given the promising response of SCN-2 towards fish habitat restoration goals, further examination/alteration of SCN-2 design aimed towards reducing sediment transport into the Swinomish Channel, while maintaining connectivity and brackish water habitat benefit, is recommended. In addition, other alternatives to modification of existing federal navigation structures should also be examined for a more complete examination of reductions in sedimentation and increased fish migration pathways.

Acknowledgments: This study was supported through a U.S. Army Corps of Engineers grant. We would like to thank David Ralston of WHOI for his collaborative support as well as sharing of site-specific monitoring data and the FVCOM code with sediment transport module. The WHOI data was collected through the Office of Naval Research Grant N00014-08-1-0846. We also appreciate continuing support from the Skagit River System Cooperative towards the development of the Skagit River estuary hydrodynamic model. Author Contributions: This paper is a collaborative effort between Pacific Northwest National Laboratory, U.S. Army Corps of Engineers, and Skagit River System Cooperative. Steve Hinton of Skagit River System Cooperative developed the preliminary designs for the McGlinn Causeway restoration project, and provided background information, historic monitoring data and design documents. Scott Brown and David Michalsen of the U.S. Army Corps of Engineers provided the bathymetric and Lidar survey data along with the design of the concepts for jetty repair scenario. Tarang Khangaonkar and Adi Nugraha of Pacific Northwest National Laboratory were responsible for all model development, application, and assessment presented in this paper. Conflicts of Interest: The authors declare no conflict of interest.

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