Prepared in cooperation with the Skagit River System Cooperative

Nearshore Circulation and Water-Column Properties 

in the Skagit River Delta, Northern Puget Sound, 

Washington

Juvenile Chinook Salmon Habitat Availability in the Swinomish Channel

Scientific Investigations Report 2007-5120

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior 

DIRK KEMPHORNE, Secretary 

U.S. Geological Survey 

Mark Myers, Director 

U.S. Geological Survey, Reston, Virginia 2007 

For product and ordering information: 

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its natural and living resources, natural hazards, and the environment: 

World Wide Web: http://www.usgs.gov 

Telephone: 1-888-ASK-USGS 

Suggested citation: 

Grossman, EE, Stevens, A, Gelfenbaum, G and Curran, C. 2007, Nearshore circulation 

and water column properties in the Skagit River Delta, northern Puget Sound, 

Washington - Juvenile Chinook salmon habitat availability in the Swinomish Channel: 

U.S. Geological Survey Scientific Investigations Report 2007-5120, 97 p. 

This report and any updates to it are available online at: 

http:pubs.usgs.gov/sir/2007/5120/ 

Any use of trade, product, or firm names is for descriptive purposes only and does 

not imply endorsement by the U.S. Government. 

Although this report is in the public domain, permission must be secured from the 

individual copyright owners to reproduce any copyrighted material contained within 

this report. 

Cover—The Swinomish Channel in La Conner, Washington. Inset shows U.S. Geological Survey instrument tripod 

used to measure circulation and water-column properties. (Photographs by E. Grossman and A. Stevens, U.S. Geological 

Survey.)
Contents 

Abstract................................................................................................................................5 

Introduction..........................................................................................................................6 

Methods................................................................................................................................9 

Tripod and Mooring Setup.............................................................................................9 

Roving ADCP Measurements of Currents...................................................................13 

Spatial Measurements of Water Column Properties derived from Conductivity, 

Temperature and Depth Profiles..................................................................................14 

Environmental Setting .................................................................................................14 

Data Processing............................................................................................................16 

Results................................................................................................................................20 

Time Series of Hydrodynamic Measurements.............................................................20 

Tides.......................................................................................................................20 

Currents..................................................................................................................22 

North Site.........................................................................................................22 

South Site.........................................................................................................33 

Cross-Channel Variability in Current Velocities—South Site ..............................43 

Water Column Properties at the Mooring..............................................................49 

Spatial Patterns in Water Properties ......................................................................52 

Spatial Salinity Gradients ......................................................................................57 

Surface Water Transport Times and Temporal Salinity Gradients........................59 

Conclusions........................................................................................................................61 

Acknowledgments..............................................................................................................62 

References Cited ................................................................................................................62 

Appendixes ........................................................................................................................63 

Appendix I. K-2-06-PS.CTD Profiles.......................................................................63 

Appendix II. K-3-06-PS.CTD Profiles. ......................................................................81 

Appendix III. K-4-06-PS.CTD Profiles......................................................................86 

Appendix IV. Metadata................................................................................................92 

2
Figures 

1. Map of study area showing instrument deployments and CTD surveys ......................7 

2. Detailed map of south Swinomish Channel showing sampling locations ...................8 

3. Photographs showing historical connections between the N. Fork Skagit River 

 and Swinomish Channel and fish passage through jetty.............................................9 

4. Photograph of the tripod deployed at the North Site, Swinomish Channel................10 

5. Photograph of the tripod deployed at the South Site, Swinomish Channel................11 

6. Photograph of the mooring deployed at Rainbow Bridge, Swinomish Channel ........11 

7. Photograph of bount-mounted “Roving” ADCP ........................................................13 

8. Photograph of Seabird 19+ profiling CTD used for spatial measurements................14 

9. Time series plot of environmental data (atmospheric pressure, wind speed, wind 

 direction, air temperature, and Skagit River discharge) during the deployment ......15 

10. Plots of wind speed and direction during the deployment........................................16 

11. Plot of acoustic doppler profiler (ADP) heading, pitch and roll at the North Site ...17 

12. Plot of acoustic doppler profiler (ADP) heading, pitch and roll at the South Site ...18 

13. Plot of water levels during the deployment ..............................................................20 

14. Plot comparing water levels between north and South Sites ....................................21 

15. Time-series plot of upper 1 m water velocity components at the north site.............23 

16. Time-series plot of depth averaged water velocity components at the north site.....24 

17. Plot of water level, current speed by tide stage, and surface and 

 depth-averaged velocities for each week of deployment at north site......................25 

18. Time-series plot of low-pass filtered along-channel current velocities and 

 cumulative along-channel transport at north site......................................................32 

19. Time-series plot of upper 1 m water velocity components at the South Site ...........34 

20. Time-series plot of depth averaged water velocity components at the South Site ...35 

21. Plot of water level, current speed by tide stage, and surface and 

 depth-averaged velocities for each week of deployment at South Site ....................36 

22. Time-series plot of low-pass filtered along-channel current velocities and 

 cumulative along-channel transport at South Site ....................................................43 

23. Cross-channel currents and backscatter profiles at south tripod site ........................44 

24. Time-series plot of temperature and salinity at the surface mooring 

 and south tripod site..................................................................................................50 

25. Plot of power spectra of temperature and salinity at the mooring 

 and south tripod sites ................................................................................................50 

26. Histogram of salinity at the mooring site..................................................................51 

27. Plot of salinity and depth along Swinomish Channel from repetitive CTD casts ....54 

28. Cross-section plot of salinity in the south Swinomish Channel for varying tides....57 

29. Map of the average spatial salinity gradient along Swinomish Channel..................58 

30. Time-series plot of surface water transport rate at the South Site and transport time 

 between McGlinn Island and Padilla Bay during the deployment ...........................59 

31. Histogram of surface water travel times between McGlinn Island and Padilla 

 Bay and associated temporal salinity gradient that exists in Swinomish Channel ...60

3
Tables 

1. Deployment information for Swinomish Channel hydrodynamic studies..................10 

2. List of instruments and their relative positions on each platform...............................12 

3. ADP Instrument Setup Information............................................................................12 

4. Date, time and burst number of first and last valid data record for each 

 instrument deployed during this experiment.............................................................19 

5. Comparison of the amplitude and phase of major harmonic tidal constituents 

 at the north (NS) and south (SS) sites.......................................................................22 

6. Environmental conditions during salinity measurements in Swinomish Channel......52 

4
Nearshore Circulation and Water-Column 

Properties in the Skagit River Delta, Northern 

Puget Sound, Washington

Juvenile Chinook salmon habitat availability in the Swinomish 

Channel 

By Eric E. Grossman, Andrew Stevens, Guy Gelfenbaum and Christopher Curran 

 

Abstract 

Time-series and spatial measurements of nearshore hydrodynamic processes and water 

properties were made in the Swinomish Channel to quantify the net direction and rates of 

surface water transport that influence habitat for juvenile Chinook salmon along their 

primary migratory corridor between the Skagit River and Padilla Bay in northern Puget 

Sound, Washington. During the spring outmigration of Skagit River Chinook between 

March and June 2006, currents measured with fixed acoustic doppler current profilers 

(ADCP) at the south and north end of the Swinomish Channel and with roving ADCP 

revealed that the currents are highly asymmetric with a dominant flow to the north 

(toward Padilla Bay). Maximum surface current velocities reached 1.5 m/s and were 

generally uniform across the channel near McGlinn Island Causeway. Transport times for 

surface water to travel the 11 km from the southern end of Swinomish Channel at 

McGlinn Island to Padilla Bay ranged from 2.1 hours to 5.5 days. The mean travel time 

was ~1 day, while 17 percent of the time, transport of water and passive particles 

occurred within 3.75 hours. Surface water in the Swinomish Channel during this time 

was generally very saline 20-27 psu, except south of the Rainbow Bridge in the town of 

La Conner where it ranged 0-15 psu depending on tide and Skagit River discharge. This 

salinity regime restricts suitable low salinity (<15-20 psu) surface waters for fry Chinook 

salmon to the southernmost 2 km of the channel. The mean change in salinity along the 

channel was 10-13 psu. The high northward current velocities have the capacity to 

transport Chinook fry into less suitable, high-salinity waters toward Padilla Bay within 

hours. The rapid transport times of 2.1 to 3.75 hours between McGlinn Island and Padilla 

Bay that occur 17 percent of the time, are considerably less than the time considered 

adequate for juvenile Chinook to acclimate and produce a temporal salinity gradient for 

pre-smolt salmon that can exceed 4 psu/hour during high northward current flow. 

5
 

Introduction 

The Swinomish Channel in Northeastern Puget Sound, Washington (figs. 1, 2), is 

considered a principal migratory corridor for juvenile and returning adult Skagit salmon 

that has lost connectivity and function due to human land use (Beamer and others, 2005.). 

Historically, the channel consisted of a network of shallow deltaic distributary channels 

(Collins, 2000) that connected the North Fork Skagit River to Swinomish Channel and 

Padilla Bay to the north. These connections provided a direct pathway for fish migration 

and an important supply of freshwater to maintain suitable salinity gradients for juvenile 

salmon smolts seeking important rearing habitat in Padilla Bay. Beginning in the 1890s, 

the channel was dredged and deepened to accommodate navigation and commercial 

transport, leading to increased tidal flow and surface salinities. In the 1930s, a causeway 

was constructed between La Connor and McGlinn Island to protect channel navigation 

from flood hazards and block sediment input to the channel from the river (fig. 3A). 

Beginning in 1938, a jetty was constructed from McGlinn Island out into Skagit Bay to 

further restrict sediment input from the river. A small fish passage retained near the 

landward edge of the jetty allows for fish passage only during high tide and/or high river 

flow (fig. 3B). It is hypothesized that Skagit Chinook experience high mortality due to 

osmotic stress as they circumvent the jetty and the high salinity waters (>15 to 20 

practical salinity units (psu)) of Skagit Bay and the Swinomish Channel as they seek 

refuge and forage habitat in Padilla Bay. Pre-smolt chinook salmon are likely unable to 

survive immediate transfer to salinities greater than 15-20 psu and suitable time to 

acclimate may take days to weeks (Healey 1991). This may explain low presence of 

Chinook along traditionally important fish habitat along the Swinomish Channel (Beamer 

and others, 2005). Although the causeway and jetty have reduced sediment infilling of 

Swinomish Channel, it is periodically dredged by the U.S. Army Corps of Engineers to 

accommodate safe navigation. Diking, dredging, and causeway/jetty development along 

the Swinomish Channel has adversely impacted habitat function across much of northern 

Puget Sound by eliminating connectivity and altering estuarine mixing processes and 

they represent a principal focus for nearshore restoration efforts throughout Puget Sound 

today. 

6
Figure 1. Map of study area showing the locations of Conductivity, Temperature, Depth 

surveys and instrument deployments (surface mooring, tripod-north and tripod-south) 

referred to in this report. Color infrared aerial photography over Swinomish Reservation 

(courtesy of Swinomish Tribe) shows false color with healthy vegetation (high reflection 

level of near-infrared wavelengths on color infrared film) appearing dark red. See later 

discussion for explanation of instruments and moorings. Inset shows area in figure 2. 

7
Figure 2. Detailed map of southern Swinomish Channel and study area showing the 

locations of Conductivity, Temperature, Depth surveys (numbers refer to casts) and 

instrument deployments (surface mooring and tripod-south) referred to in this report. See 

later discussion for explanation of instruments and moorings.

8
A 

 

 

B 

Figure 3. (A) Annotated 1937 aerial photograph showing sloughs that connected the N. 

Fork Skagit River to Swinomish Channel prior to infilling of McGlinn Island Causeway and 

construction of the Skagit Bay jetty. (B) The only fish passage for juvenile Skagit Chinook 

Salmon to Swinomish Channel is usable only at high tides. 

This report presents data from hydrodynamic and water property measurements made 

in the Swinomish Channel and Skagit Bay during the Spring 2006 outmigration of Skagit 

Chinook salmon. This effort was made to quantify the nearshore circulation patterns, 

current velocities, and water properties that influence habitat availability for juvenile 

salmonids using the Swinomish Channel. These data enable calculations to be made of 

the volume of freshwater needed to sustain suitable salinity gradients for juvenile 

salmonids, particularly Chinook that require longer time to adjust to saline water, and to 

calculate transport times of water and juvenile/fry salmon through the channel. This 

information will help to evaluate possible restoration alternatives aimed to re-establish 

historical migratory connectivity between the Skagit River and essential rearing habitat in 

Padilla Bay and to design refuge habitats along the channel for fish to escape the high 

current velocities and adequately adjust to the increased salinities of northern Swinomish 

Channel and Padilla Bay. 

Methods 

Tripod and Mooring Setup 

Two instrumented tripods equipped to measure currents and water properties were 

deployed on the north and south side of the Swinomish channel (figs. 1 and 2) for a 1.5 

month period between March and May of 2006 (table 1). Each tripod was equipped with 

9
a Sontek 1500 kHz Acoustic Doppler Profiler (ADP). Water temperature was measured 

at the north tripod using a Brancker temperature sensor. At the South Site, a Seabird SB37 Microcat recorded temperature, conductivity, and pressure. Each tripod had a retrieval 

system consisting of an Edgetech Cart acoustic release connected to a line and buoy. An 

acoustic pinger was placed on the tripod to aid in its recovery in the event that the release 

system failed. Figures 4 and 5 show photos of the two instrumented tripods immediately 

before deployment at the north and South Site, respectively. 

Table 1. Deployment information for Swinomish Channel hydrodynamic studies. 

 North Site South Site Surface Mooring 

Deployment Date 3/28/2006 3/28/2006 3/29/2006 

Deployment Latitude 48.4443 °N 48.3768 °N 48.38722 °N 

Deployment Longitude 122.5078 °W 122.5086 °W 122.50125 °W 

Recovery Date 5/16/2006 5/16/2006 5/16/2006 

Figure 4. Photograph of the tripod deployed at the North Site, Swinomish Channel. 

10
Figure 5. Photograph of the tripod deployed at the South Site, Swinomish Channel. 

Continuous temperature and salinity measurements of the surface water were made 

with a Seabird SB-37 Microcat attached to a surface mooring (fig. 6). The mooring 

consisted of a Gilman 4CFR buoy with a Carmanah solar light attached to the top. The 

microcat was fixed to the mooring to measure temperature and salinity 50 cm below the 

surface. The mooring was deployed near the Rainbow Bridge between the two tripods to 

detect northward advection of freshwater from the N. Fork Skagit River. Table 2 reports 

the instruments deployed and their positions relative to the bottom of the tripod. 

 

Figure 6. Photograph of the mooring deployed at Rainbow Bridge, Swinomish Channel. 

11
Table 2. List of instruments and their relative positions on each platform. 

Station Instrument Serial Number Height (cmab) 

ADP C134 134.5 

North Site 

Branker Temp. Sensor 6992 108.0 

ADP C132 135.0 

South Site 

SB-37 Microcat 283 64.5 

Surface Mooring SB-37 Microcat 1700 35.0* 

* The reported height of the SB-37 microcat attached to the surface mooring is cm below water surface. 

SonTek acoustic Doppler profilers (ADPs) are designed to measure profiles of velocity 

throughout the water column. The sampling scheme for the current meters was designed 

in order to obtain accurate measurements in a region known to have relatively high 

current velocities and provide high resolution vertically in the water column. The current 

meters were set to average current measurements for a 5 min period to produce a current 

profile every 15 min. The start of each burst was set to begin 2.5 min before each quarterhourly measurement. The vertical cell size was set to 0.25 m beginning 0.4 m from the 

transducer. Table 3 includes the sampling setup parameters for the two current profilers. 

Table 3. Acoustic Doppler Profiler instrument setup information. 

Parameters North Site South Site 

ADP Serial Number C134 C132 

Frequency (kHz) 1500 1500 

Cell size (m) 0.25 0.25 

Blanking distance (m) 0.4 0.4 

Number of cells 60 60 

Ensemble interval (min) 15 15 

Averaging interval (min) 5 5 

Coordinate System ENU ENU 

Time Zone GMT GMT 

Magnetic Declination (degrees) 17.8 17.8 

The ADPs also measured water temperature and pressure. An internal compass and 

two-axis tilt sensor measured heading, pitch and roll. Using the measurements of the 

compass (heading, tilt and roll), velocity measurements were transformed and stored in 

12
geographic components of velocity (east, north, up). Both tripods were recovered using 

an Edgetech Coastal Acoustic Release Transponder (CART ) and buoy system. Upon 

recovery, both tripods had relatively little bio-fouling and all instruments appeared to be 

in good condition. The south tripod was estimated to have sunk into the sediment to a 

depth of 30-40 cm based on the complete lack of fouling on the lower legs of the tripod. 

On the north tripod, the depth of burial was unable to be determined because very little 

fouling occurred on the entire tripod. 

Roving ADCP Measurements of Currents 

Cross-channel variability in currents were measured with a boat-mounted 600 kHz Rio 

Grande Workhorse Acoustic Doppler Current Profiler (ADCP) and a Trimble Ag 132 

DGPS that achieves sub-meter positional accuracy (fig. 7). The bottom-tracking ADCP 

was operated continuously with a ping rate of 5 Hz, vertical cell size of 0.5 m, and a 0.25 

m blanking distance (distance from the transducer). The velocity, depth, temperature and 

position data were acquired and processed with WinRiver firmware version 10.14 ADCP 

software, averaging 3 pings per ensemble following Oberg and others, (2005). Boat speed 

ranged 3-6 kts, such that resulting processed current measurements span 1-2 m along 

track. 

Figure 7. Photograph of the roving Acoustic Doppler Current Profiler and 

Differential Geographic Positioning System setup. 

13
Spatial Measurements of Water Column Properties derived from 

Conductivity, Temperature and Depth Profiles 

Water column properties including conductivity (converted to salinity), temperature, 

salinity, and depth (CTD) were measured at stations along the Swinomish Channel in 

March, May, and July 2006 (figs. 1 and 2) with a Seabird Electronics model 19+ 

Profiling CTD (fig. 7). The Seabird 19+ operates at 4 Hz and downcasts were conducted 

manually at an approximate rate of 1 m/10 sec to acquire at least 10 samples per 0.25 m. 

In addition to conductivity, temperature, and depth, turbidity, dissolved oxygen, 

photosynthetically active radiation, and chlorophyll were measured and average sound 

velocity was derived. Locations and times of CTD casts were obtained with a Garmin 

GPS. 

Figure 8. Photograph of Seabird 19+ profiling Conductivity, Temperature, and Depth 

sensor used for spatial measurements. 

Environmental Setting 

Atmospheric pressure, wind speed and direction, and air temperature during the 

Swinomish Channel deployment were obtained from the Whidbey Island Naval Air 

Station (USAF-WBAN_ID 690230 24255, http://www4.ncdc.noaa.gov/cgiwin/wwcgi.dll?wwDI~StnSrch~StnID~20027920). Wind direction was changed to the 

oceanographic convention whereby direction refers to the direction wind is flowing to. 

Skagit River discharge was obtained from the U.S. Geological Survey (USGS) Mount 

Vernon gauge station (Station 12200500, 

http://waterdata.usgs.gov/wa/nwis/uv/?site_no=12200500&). 

14
Weather conditions during the deployment were characteristic of slow warming and 

rise in air pressure associated with the transition from early to late spring (fig. 9). Winds 

generally ranged 0-7 m/s and from the west and southeast (fig. 10) except for passing low 

pressure systems. Two significant low pressure systems during the middle of April and 

early May led to increases in wind velocities (10-15 m/s) originating from the eastsoutheast. Skagit River discharge ranged 1,000-2,000 cubic feet per second (cfs) during 

most of the deployment and began to rise toward spring flood levels near the end of our 

deployment. 

Figure 9. Time series of environmental data collected at the Whidbey Island 

meteorological station. Wind direction refers to the direction the wind is flowing to. River 

discharge is measured at the Mt. Vernon gauge (Station 12200500). 

15
Figure 10. Plot of (A) wind speed (in m/s) and direction during the Swinomish Channel 

deployment. (B) Histogram of wind direction. Wind direction refers to the direction the 

wind is flowing to. 

Data Processing 

High quality data were recovered from all of the instruments deployed in this study. 

However, problems with the analog to digital converter (B. Macone, Sontek, oral 

commun.) resulted in bad pressure and temperature data recorded by ADP C132 at the 

South Site. Fortunately, the South Site tripod was also equipped with a SBE-37 microcat 

that made temperature and pressure measurements. 

Data collected by the compass and 2-axis tilt sensor in the ADP suggest minor 

movement of both tripods within the first ~2 days of deployment as the tripod settles into 

the bed (figs. 11 and 12). Afterwhich, the heading, pitch and roll changed only gradually, 

suggesting that neither of the tripods were significantly disturbed during data collection. 

16
Figure 11. Time-series of heading, pitch and roll collected by the internal compass of the 

acoustic Doppler profiler (ADP) at the North Site. °M, degrees from magnetic north. 

17
Figure 12. Time-series of heading, pitch and roll collected by the internal compass of the 

acoustic Doppler profiler (ADP) at the South Site. °M, degrees from magnetic north. 

Time periods where valid data were collected were determined by visual inspection of 

the pressure as well as heading, pitch and roll time-series data. Data points recorded when 

the instruments were out of the water were removed from the record. Table 4 shows the 

periods when valid data were recorded for each instrument. 

18
Table 4. Date, time and burst number of first and last valid data record for each instrument 

deployed during this experiment.

Start End 

Station Instrument Sample Date Time Sample Date Time 

ADP 1 3/28/2006 22:27:30 4688 5/16/2006 18:12:30 

North 

Site Branker 

Temp. 

Sensor 

678 3/28/2006 22:34:00 35840 5/16/2006 18:38:00 

ADP 1 3/28/2006 20:57:30 4612 5/15/2006 21:42:30 South 

Site SB-37 

Microcat 1235 3/28/2006 20:43:01 70435 5/15/2006 22:03:01 

Surface 

Mooring 

SB-37 

Microcat 1449 3/29/2006 00:08:03 71612 5/16/2006 17:31:02 

After nonvalid data points were removed, the raw data files were exported to ascii text 

files using Sontek’s ViewAdp Pro software. The ascii files were read into a matlab data 

structure for further analysis. The east and north components of velocity were rotated to 

account for the site-specific variation in magnetic declination at the time of the 

deployment (17.8 °E). 

A script in MATLAB was written to use the pressure sensor in the ADP to find and 

remove bins that were above the water surface. Water depth was determined by assuming 

that 1 dbar of pressure was equal to 1 m of water vertically in the water column. If the 

center of the bin did not fall below the defined surface, that bin and all bins above it were 

removed from the data record. In the case of the South Site ADP, where internal pressure 

data were bad, data from the microcat were used (after correcting for the vertical offset 

between the two instruments, 70.5 cm) to remove out-of-water bins. 

In order to investigate net water movement in the channel, velocities in three layers 

were rotated into along- and across- channel components using principle component 

analysis (PCA). A standard (33-hr) low-pass filter was then applied to the rotated 

velocities to plot current patterns occurring at subtidal frequencies. Cumulative alongchannel transport was calculated by taking the cumulative sum of the product of the 

along-channel velocity component and ∆t (15 min or 900 s). 

CTD measurements were processed with standard Seabird protocols using Seabird 

calibrations and correcting for surface soak and instrument priming. Measurements were 

averaged at 0.25 m depth intervals and merged with navigation, environmental data (tide 

stage, winds, river discharge), and current measurements. Analyses of CTD casts 

including cross-sections and surface maps were made using Matlab and ArcMap nearest 

neighbor grid algorithms. Plots of all casts are provided in appendices I-III.

19
Results 

Time Series of Hydrodynamic Measurements 

Tides 

The tidal height at the north site was measured using the internal pressure sensor in the 

ADP. At the South Site, where pressure data were corrupt, pressure data from the 

microcat were used to estimate water levels. Water level at each site was estimated by 

assuming that each dbar of pressure represents one meter of water depth. Reported water 

level values (fig. 13) are relative to the mean water level at each site during the 

deployment (that is, the mean was removed from each time-series to compare water 

levels). 

Figure 13. Water levels relative to the mean water height during the deployment for the 

north (top panel) and south (bottom panel) tripods. 

Comparison of the water levels at the two sites (fig. 14) suggests that the amplitude of 

the tidal oscillations is larger at the South Site compared to the North Site. The 

instantaneous difference in tidal elevation is as high as 0.5 m at some times during the 

20
deployment (fig. 14, middle panel). Positive values indicate the water level was higher at 

the South Site relative to the North Site. Low-pass filtered differences in tidal elevation 

(fig. 14, bottom panel) show that the water level at the South Site is higher at subtidal 

frequencies throughout most of the data record. 

 

Figure 14. Comparison of water levels between the North and South Sites (top panel). The 

middle and bottom panel show the difference (South Site-North Site) and low-pass filtered 

(LPF) difference between the two sites, respectively. 

Harmonic analysis on each of the water level time-series was carried out using the 

T_Tide analysis package for MATLAB (Pawlowicz and others, 2002). Comparison of the 

21
major harmonic constituents at each site (table 5) shows that the amplitude of the two 

biggest components, K1 and M2, are larger at the South Site than at the North Site. Also, 

there are differences in the phase of major tidal components between the two sites. For 

instance, a phase difference of 4.3 degrees for the M2 constituent equates to about a 9 

min difference between the two sites. 

Table 5. Comparison of the amplitude and phase of major harmonic tidal constituents at 

the north (NS) and south (SS) sites. 

Constituent Frequency 

[1/hr] 

NS 

Amplitude 

[m] 

SS 

Amplitude 

[m] 

N-S 

Amplitude 

Diff. [m] 

NS 

Phase 

[deg] 

SS 

Phase 

[deg] 

N-S 

Phase Diff 

[deg] 

Q1 0.0372 0.076 0.073 0.003 231.7 231.9 -0.2 

O1 0.0387 0.494 0.498 -0.004 254.7 253.3 1.4 

K1 0.0418 0.800 0.823 -0.023 268.0 268.4 -0.4 

J1 0.0433 0.037 0.036 0.001 319.0 323.3 -4.3 

N2 0.0790 0.150 0.189 -0.039 336.6 337.5 -0.9 

M2 0.0805 0.725 0.923 -0.198 15.7 19.9 -4.2 

L2 0.0820 0.025 0.037 -0.012 77.1 97.9 -20.8 

S2 0.0833 0.199 0.271 -0.072 31.8 35.4 -3.6 

M3 0.1208 0.006 0.009 -0.003 235.5 213.9 21.6 

M4 0.1610 0.007 0.012 -0.005 297.6 311.9 -14.3 

S4 0.1667 0.001 0.002 -0.001 261.5 300.5 -39 

2MK5 0.2028 0.012 0.017 -0.005 131.2 106.9 24.3 

M6 0.2415 0.012 0.018 -0.006 215.9 146.8 69.1 

Currents 

North Site 

Maximum horizontal velocities at the north site were 57.7 and 108.5 cm/s for the u- and 

v- components of velocity, respectively. Vertical velocities were always less than 10 cm/s 

and typically less than 5 cm/s. The maximum observed current speed at the surface was 

115 cm/s (fig. 15), whereas the maximum depth-averaged current magnitude was 109 

cm/s (fig. 16). The direction of the currents was primarily in the along-channel directions 

of 330° (toward Padilla Bay) and 150° (toward La Conner/ Skagit Bay). 

Current speed and direction for each week of the deployment shows in detail the 

vertical structure of currents in the water column throughout the deployment (fig. 17AG). Current speeds do not appear to closely match the range of a given tide, nor does the 

direction of the current switch exclusively at high and low tide. That is, slack water is not 

exclusively occurring at the crest and trough of the tidal cycle. Also, the current is 

asymmetric, typically flowing toward the northwest for a longer period than it does to the 

southeast. 

22
The low-pass filtered, along-channel velocities (fig. 18) indeed show net transport to 

the northwest toward Padilla Bay, with only brief periods where net transport was 

directed to the southeast. Over the course of the 1.5 month deployment, net along-channel 

transport for the top 1-m was around 250 km. As would be expected in a confined 

channel, cross-channel net transport was negligible. 

Figure 15. Time-series of u (positive eastward), v (positive northward), and w (positive up) 

velocity components, speed and direction for the top 1 m of the water column at the North 

Site. Low-pass filtered data (red lines) show the trends occurring at subtidal (> 33 hr) 

frequencies. °T, degrees from true north. 

23
Figure 16. Time-series of u (positive eastward), v (positive northward), and w (positive up) 

velocity components, speed and direction averaged over the water column at he North 

Site. Low-pass filtered data (red lines) show the trends occurring at subtidal (> 33 hr) 

frequencies. °T, degrees from true north.

24
Figure 17A. Data from the North Site Acoustic Doppler Profiler during the week of 3/28 and 

4/04 (gray box, top panel). The middle panel shows current speed in each 0.25-m bin 

throughout the water column. The bottom panel shows surface (red lines) and depthaveraged (blue lines) current vectors. 

25
Figure 17B. Data from the North Site Acoustic Doppler Profiler during the week of 4/04 and 

4/11 (gray box, top panel). The middle panel shows current speed in each 0.25-m bin 

throughout the water column. The bottom panel shows surface (red lines) and depthaveraged (blue lines) current vectors. 

26
Figure 17C. Data from the North Site Acoustic Doppler Profiler during the week of 4/11 and 

4/18 (gray box, top panel). The middle panel shows current speed in each 0.25-m bin 

throughout the water column. The bottom panel shows surface (red lines) and depthaveraged (blue lines) current vectors. 

27
Figure 17D. Data from the North Site Acoustic Doppler Profiler during the week of 4/18 and 

4/25 (gray box, top panel). The middle panel shows current speed in each 0.25-m bin 

throughout the water column. The bottom panel shows surface (red lines) and depthaveraged (blue lines) current vectors. 

28
Figure 17E. Data from the North Site Acoustic Doppler Profiler during the week of 4/25 and 

5/02 (gray box, top panel). The middle panel shows current speed in each 0.25-m bin 

throughout the water column. The bottom panel shows surface (red lines) and depthaveraged (blue lines) current vectors. 

29
Figure 17F. Data from the North Site Acoustic Doppler Profiler during the week of 5/02 and 

5/09 (gray box, top panel). The middle panel shows current speed in each 0.25-m bin 

throughout the water column. The bottom panel shows surface (red lines) and depthaveraged (blue lines) current vectors. 

30
Figure 17G. Data from the North Site Acoustic Doppler Profiler during the week of 5/09 and 

5/16 (gray box, top panel). The middle panel shows current speed in each 0.25-m bin 

throughout the water column. The bottom panel shows surface (red lines) and depthaveraged (blue lines) current vectors. 

31
Figure 18. Time-series of low-pass filtered, along-channel velocity (top panel) for the 

surface (blue line), depth-averaged (red line) and bottom (black line) portion of the water 

column at the North Site. Positive values indicate northward transport (toward Padilla 

Bay) while negative values indicate net southward transport (toward Skagit Bay). The 

bottom panel shows the cumulative along-channel transport of water for the surface, 

depth-averaged and bottom. The surface values are representative of the top 1 m 

whereas the bottom represents the bottom 4 bins (1 m) measured by the Acoustic Doppler 

Profiler. 

32
South Site 

 

Maximum horizontal velocities at the South Site were 92.2 and 97.8 cm/s for the u- and 

v- components of velocity, respectively. Vertical velocities did not exceed 10 cm/s and 

were generally less than 5 cm/s. The maximum observed current speed at the surface was 

133 cm/s (fig. 19) while the maximum depth-averaged current speed was 113 cm/s (fig. 

20). The direction of the currents was primarily in the along-channel directions of 37° 

(toward Padilla Bay) and 215° (toward La Conner/ Skagit Bay). 

Current speed and direction for each week of the deployment shows in detail the 

vertical structure of currents in the water column throughout the deployment (fig. 21AG). Similarly to the north site, current speeds do not appear to closely match the range of 

a given tide, nor does the direction of the current switch exclusively at high and low tide. 

Also similar to the north site, the current at the South Site is asymmetric, flowing toward 

the northwest for a longer period than it does to the southeast. 

The low-pass filtered, along-channel velocities at the South Site (fig. 22) show net 

transport to the northwest toward Padilla Bay, with only brief periods where net transport 

was directed to the southeast. Over the course of the 1.5-month deployment, net alongchannel transport for the top 1-m was nearly 400 km. As would be expected in a confined 

channel, cross-channel net transport was negligible. 

33
Figure 19. Time-series of u (positive eastward), v (positive northward), and w (positive up) 

velocity components, speed and direction for the top 1 m of the water column at the South 

Site. Low-pass filtered data (red lines) show the trends occurring at subtidal (> 33 hr) 

frequencies. °T, degrees from true north. 

34
Figure 20. Time-series of u (positive eastward), v (positive northward), and w (positive up) 

velocity components, speed and direction averaged over the water column at the South 

Site. Low-pass filtered data (red lines) show the trends occurring at subtidal (> 33 hr) 

frequencies. °T, degrees from true north. 

35
Figure 21A. Along-channel velocity from the Acoustic Doppler Profiler at the South Site 

during the week of 3/28 and 4/04. The middle panel shows current speed in each 0.25-m 

bin throughout the water column. The bottom panel shows surface (red lines) and depthaveraged (blue lines) current vectors. 

36
Figure 21B. Along-channel velocity from the Acoustic Doppler Profiler at the South Site 

during the week of 4/04 and 4/11 (gray box, top panel). The middle panel shows current 

speed in each 0.25-m bin throughout the water column. The bottom panel shows surface 

(red lines) and depth-averaged (blue lines) current vectors. 

37
Figure 21C. Along-channel velocity from the Acoustic Doppler Profiler at the South Site 

during the week of 4/11 and 4/18 (gray box, top panel). The middle panel shows current 

speed in each 0.25-m bin throughout the water column. The bottom panel shows surface 

(red lines) and depth-averaged (blue lines) current vectors. 

38
Figure 21D. Along-channel velocity from the Acoustic Doppler Profiler at the South Site 

during the week of 4/18 and 4/25 (gray box, top panel). The middle panel shows current 

speed in each 0.25-m bin throughout the water column. The bottom panel shows surface 

(red lines) and depth-averaged (blue lines) current vectors. 

39
Figure 21E. Along-channel velocity from the Acoustic Doppler Profiler at the South Site 

during the week of 4/25 and 5/02 (gray box, top panel). The middle panel shows current 

speed in each 0.25-m bin throughout the water column. The bottom panel shows surface 

(red lines) and depth-averaged (blue lines) current vectors. 

40
Figure 21F. Along-channel velocity from the Acoustic Doppler Profiler at the South Site 

during the week of 5/02 and 5/09 (gray box, top panel). The middle panel shows current 

speed in each 0.25-m bin throughout the water column. The bottom panel shows surface 

(red lines) and depth-averaged (blue lines) current vectors. 

 

41
Figure 21G. Along-channel velocity from the Acoustic Doppler Profiler at the South Site 

during the week of 5/09 and 5/15 (gray box, top panel). The middle panel shows current 

speed in each 0.25-m bin throughout the water column. The bottom panel shows surface 

(red lines) and depth-averaged (blue lines) current vectors. 

42
Figure 22. Time-series of low-pass filtered, along-channel velocity (top panel) for the 

surface (blue line), depth-averaged (red line) and bottom (black line) portion of the water 

column at the South Site. Positive values indicate northward transport (toward Padilla 

Bay) while negative values indicate net southward transport (toward Skagit Bay). The 

bottom panel shows the cumulative along-channel transport of water for the surface, 

depth-averaged and bottom. The surface values are representative of the top 1 m while 

the bottom represents the bottom 4 bins (1 m) measured by the Acoustic Doppler Profiler. 

Cross-Channel Variability in Current Velocities—South Site 

Peak current velocities measured across the channel with the roving ADCP agree well 

with currents measured at the south tripod site and show that current speed and directions 

are generally uniform across most of the channel. Figures 23A-C show that during 

flooding of a spring tide condition, surface current velocities range 1.3 to 1.5 m/s across 

most of the channel at the Hole in the Wall site, except for the west edge of the channel 

where shear occurs and eddys can form. These high current speeds also occur down 2-4 

m across most of the channel and to the seafloor in the deepest section of the channel at 

the Hole in the Wall. 

43
Figure 23A. (Top) Map of surface current velocity and direction across the South Site 

during flood of spring tide condition of June 12, 2006 (white box start of transect). (Bottom 

three plots) Cross-channel current velocity, direction, and backscatter with depth. 

44
Figure 23B. (Top) Map of surface current velocity and direction across the South Site 

during flood of spring tide condition of June 12, 2006 (white box start of transect). (Bottom 

three plots) Cross-channel current velocity, direction, and backscatter with depth.

45
Figure 23C. (Top) Map of surface current velocity and direction across the South Site 

during flood of spring tide condition of June 12, 2006 (white box start of transect). (Bottom 

three plots) Cross-channel current velocity, direction and backscatter with depth.

46
Figure 23D. (Top) Map of surface current velocity and direction 150 m north of the South 

Site during flood of spring tide condition of June 12, 2006 (white box start of transect). 

(Bottom three plots) Cross-channel current velocity, direction and backscatter with depth.

47
Figure 23E. (Top) Map of surface current velocity and direction 150 m north of the South 

Site during flood of spring tide condition of June 12, 2006 (white box start of transect). 

(Bottom three plots) Cross-channel current velocity, direction and backscatter with depth. 

48
A second set of cross-channel profiles approximately 150 m north (figs. 23D-E) are 

characterized by slightly higher current velocities and more uniform directions. 

Backscatter intensity, reflecting suspended particle concentration in the water column, is 

high and relatively uniform across the channel under high current velocities. Figures 23AD show isolated regions of higher backscatter between 1 and 3 m depth. It is unclear if 

these are transient features or persistent areas of high suspended particulate 

concentration. 

Water Column Properties at the Mooring 

The SBE-37 microcat attached to the surface mooring at roughly 35 cm below the 

surface recorded temperatures ranging from 7.3–13.9°C while temperatures on the 

bottom at the South Site varied between 7.4–13.2°C (fig. 24, top panel). Temperatures 

were typically slightly higher at the surface compared to the bottom (0.16°C on average) 

and were as much as 2°C higher at times. A general warming trend at both the surface 

and bottom was observed throughout the deployment. 

Salinities measured at the surface mooring ranged from 9 to 26 practical salinity units 

(psu) with a mean of 20.9 psu (fig. 24, bottom panel). At the South Site, salinities 

measured at roughly 64.5 cm above the bed vary between 13 to 27 psu. The surface water 

salinity is typically lower than the near bottom salinities recorded at the South Site. Low 

frequency fluctuations in salinity at both sites are minor except during one time-period 

between April 12 and April 19 when salinity was fresher compared to the rest of the 

deployment. 

In both the temperature and salinity records, high-frequency fluctuations were 

important in addition to longer term trends. The power spectral density of the temperature 

and salinity time-series were calculated using Welch's averaged modified periodogram 

method of spectral estimation. These spectra (fig. 25) indicate that the higher frequency 

fluctuations in both the temperature and salinity time-series are occurring at frequencies 

close to the major diurnal (K1, 23.9 hr) and semi-diurnal (M2, 12.4 hr) constituents. 

However, the temperature time-series is dominated by a diurnal signal, suggesting diurnal 

heating and cooling plays an important role. The salinity time-series shows a stronger 

influence of semi-diurnal (M2) and other shorter frequency fluctuations (M3, M4, 2MK5 

and M6). During these tide variations, flood tides advect lower salinity water to the 

mooring site generally in the 15 to 20 psu range; occasionally spikes as low as 8-10 psu 

occur (fig. 24). 

49
Figure 24. Time-series of temperature and salinity at the surface mooring (blue lines) and 

at the South Site (red lines). 

Figure 25. Power spectral density of temperature (left panel) and salinity (right panel) at 

the surface mooring (blue lines) and tripod (red lines). 

50
A histogram shows that 66 percent of the time salinity ranged from 20 to 25 psu, 

whereas salinities lower than 15 were observed less than 3 percent of the data record. 

Thirty percent of the time surface salinity at the mooring site ranged from 15 to 20 psu. 

Figure 26. Normalized histogram of salinity at the mooring site. 

51
Spatial Patterns in Water Properties 

Repeat measurements water column profile of temperature and salinity throughout the 

area reveal that north of the Rainbow Bridge in La Conner, salinities between March and 

July were generally higher than 23 psu and water was relatively well mixed throughout 

the Swinomish Channel (fig. 27A,B; see figs. 1 and 2 for locations). Between Shelter Bay 

and the Rainbow Bridge, salinities were slightly lower 20-22 psu (figs. 27C,D), with an 

occasional thin (<1-3 m) fresher surface lens occurring only during peak flooding tides 

(K206PS_037, ~110 cm/sec) or high river flow (K306PS_009, 20,973 cfs; K306PS_012, 

21,107 cfs; k406ps_003, 13,253 cfs) (see table 6 for environmental conditions at time of 

CTD profiling). Exceptions to this pattern exist with mixing of moderately saline (23 psu) 

water through the water column despite a modest flooding tide and river discharge 

(K206PS_024, 73 cm/sec flood tide currents, 11,250 cfs). 

The only appreciable low salinity surface lenses occur between the Fish Passage near 

station 3B and the south tripod station (figs. 27E,F). At the south tripod station, salinities 

in the upper 3 m reached as low as 18 psu and showed a slightly fresher surface lens in 50 

percent of the casts made. These conditions were generally associated with high river 

discharge (K306PS_011, 21,107 cfs) but also occur during only modest river discharge 

and during ebbing tides (fig. 27E) suggesting that lower salinity lenses (18-20 psu) may 

temporarily extend north of the south tripod site and are advected back to the south 

during reversal of flow. Only station 3B showed any appreciable low salinity surface 

water lens (fig. 27f). Salinity at station 3B typically ranged 12-25 psu and reached as low 

as 6 psu on one occasion during an ebb tide also suggesting that low salinity surface 

water is periodically advected southward during flow reversals away from the net 

northward regime. The low-salinity surface water lens was generally found to be only 1-2 

m thick in this part of the Swinomish Channel. 

 

Table 6. Environmental conditions during salinity measurements in Swinomish Channel. 

Tide Tide River Flow Current Direction 

Filename Local Time (m) State* (cfs) (cm/s) (degrees) 

TRP-N 

k206ps_004 3/28/2006 14:30 2.89 floodLH 11406 1.43 92.6 

k206ps_030 3/29/2006 15:13 2.69 floodLH 10222 17.52 331.73 

k306ps_005 5/15/2006 11:34 -0.24 ebbLL 16308 11.83 144.29 

Dock 

k206ps_001 3/28/2006 8:30 1.29 ebbHL 14962 N/A N/A 

k206ps_006 3/29/2006 8:32 1.39 ebbLL 11629 3.13 346.65 

k206ps_027 3/29/2006 11:47 0.58 floodLH 11162 69.89 212.99 

k206ps_028 3/29/2006 14:11 1.95 floodLH 10460 11.62 39.91 

k206ps_046 3/29/2006 17:51 3.24 ebbHL 9900 88.37 40.73 

k206ps_047 3/30/2006 8:03 2.15 ebbLL 10286 27.76 37.34 

k206ps_065 3/30/2006 10:33 0.16 ebbLL 10179 66.89 213.57 

k306ps_003 5/15/2006 10:01 0.83 ebbLL 16086 27.9 216.24 

52
k306ps_008 5/16/2006 9:30 1.72 ebbLL 20627 N/A N/A 

k306ps_014 5/16/2006 11:41 0.19 ebbLL 21241 N/A N/A 

k406ps_001 7/26/2006 5:51 2.6 ebbLL 13346 N/A N/A 

k406ps_018 7/26/2006 11:17 -0.42 turningLL 11295 N/A N/A 

Bridge 

k206ps_005 3/28/2006 16:15 3.23 ebbHL 10897 97.85 40.93 

k206ps_036 3/29/2006 16:30 3.35 floodLH 10028 90.48 38.73 

k206ps_045 3/29/2006 17:35 3.36 ebbHL 9900 94.57 40.65 

k206ps_064 3/30/2006 10:20 0.16 ebbLL 10200 66.89 213.57 

k306ps_004 5/15/2006 10:49 0.08 ebbLL 16160 48.31 211.65 

k306ps_009 5/16/2006 10:41 0.95 ebbLL 20973 N/A N/A 

k406ps_002 7/26/2006 6:11 2.6 ebbLL 13253 N/A N/A 

k406ps_017 7/26/2006 10:58 -0.38 ebbLL 11406 N/A N/A 

Shelter Bay 

k206ps_024 3/29/2006 11:15 0.4 floodLH 11250 73.15 213.37 

k206ps_037 3/29/2006 16:39 3.35 floodLH 9985 109.95 40.31 

k306ps_012 5/16/2006 11:17 0.19 ebbLL 21107 N/A N/A 

k406ps_003 7/26/2006 6:21 2.36 ebbLL 13253 N/A N/A 

k406ps_016 7/26/2006 10:51 -0.38 ebbLL 11495 N/A N/A 

TRP-S 

k206ps_008 3/29/2006 9:01 1 ebbLL 11607 18.71 214.86 

k206ps_022 3/29/2006 11:00 0.31 turningLL 11295 69.85 211.51 

k206ps_039 3/29/2006 16:54 3.4 turningLH 9964 106.59 42.6 

k206ps_048 3/30/2006 8:37 1.69 ebbLL 10222 6.04 22.12 

k206ps_063 3/30/2006 10:08 0.44 ebbLL 10200 53.3 211.4 

k306ps_001 5/14/2006 15:02 0.62 floodHH 11945 1.33 73.07 

k306ps_011 5/16/2006 11:10 0.56 ebbLL 21107 N/A N/A 

k406ps_004 7/26/2006 6:28 2.36 ebbLL 13230 N/A N/A 

k406ps_015 7/26/2006 10:45 -0.38 ebbLL 11495 N/A N/A 

3B 

k206ps_011 3/29/2006 9:24 0.68 ebbLL 11540 50.89 215.71 

k206ps_020 3/29/2006 10:45 0.31 turningLL 11361 68.42 212.45 

k206ps_040 3/29/2006 17:00 3.4 turningLH 9964 106.59 42.6 

k206ps_049 3/30/2006 8:45 1.24 ebbLL 10222 6.04 22.12 

k206ps_058 3/30/2006 9:40 0.81 ebbLL 10200 42.95 214.02 

k206ps_059 3/30/2006 9:44 0.81 ebbLL 10200 42.95 214.02 

k306ps_010 5/16/2006 11:03 0.56 ebbLL 21000 N/A N/A 

k406ps_006 7/26/2006 6:39 2.36 ebbLL 13183 N/A N/A 

k406ps_013 7/26/2006 10:36 -0.25 ebbLL 11607 N/A N/A 

*Tide State: FloodLH= flooding from lowest semi-diurnal low tide to highest semi-diurnal high tide of the day. 

 ebbLL=ebbing from lowest semi-diurnal high tide to lowest semi-diurnal low tide of the day. 

 turningLL=turning from lowest semi-diurnal low tide of the day. 

 floodHH=flooding from highest semi-diurnal low tide to highest semi-diurnal high tide of the day. 

 turningLH=turning from lowest semi-diurnal high tide of the day. 

53
Figure 27A. Variability in salinity at station TRPN. 

Figure 27B. Variability in salinity at station Dock. 

54
Figure 27C. Variability in salinity at station Bridge. 

Figure 27D. Variability in salinity at station Shelter Bay. 

55
Figure 27E. Variability in salinity at station TRP-S. 

Figure 27F. Variability in salinity at station 3B. 

 

A slight limitation of this data is the coverage of CTD profile data which span a greater 

range of ebb tide conditions than flood. It is likely that lower salinity surface water 

extends northward for greater duration of time than observed with these casts, but is 

56
limited to the area between the south tripod station and the bridge as indicated by the 

time-series data collected by the surface mooring. These results are consistent with those 

found by Yates (2001) who also observed low salinity zones restricted to the region near 

the jetty and Hole in the Wall. 

Spatial Salinity Gradients 

 

Spatial salinity gradients are difficult to depict as processes continuously modify them. 

Even so, mean conditions are useful to portray dominant patterns and examine temporal 

variability around the mean. The only suitable salinity gradients for juvenile Chinook 

during the study period were restricted to the southern Swinomish Channel as shown by 

the mooring and in two different CTD surveys in July during modest river discharge 

(13,253 cfs) and ebb tide conditions (fig. 28). In these two cases, the low salinity surface 

lens was restricted to the region south of the Hole in the Wall where salinities ranged 

between 8 and ~18 psu. During flood conditions this low salinity lens is advected 

northward along with saline water from Skagit Bay. Depending on river discharge level, 

current velocities and possibly local wind patterns, these water masses are largely mixed 

by the south tripod site and only during the highest river flows and flood currents do low 

salinity lenses extend to the Rainbow Bridge (fig. 24). 

Figure 28. (A) Map of stations used to produce cross-section plots in (B). (B) Crosssection plots of salinity gradients between the Rainbow Bridge and station 4B (seaward of 

the Fish Passage) at two different tidal elevations. The grey lines indicate the length of 

time when the CTD transects were performed. 

57
The average spatial salinity gradient that existed between McGlinn Island and Padilla 

Bay during the conditions characterizing our mooring deployment and CTD profiling 

surveys between March and July, 2006 was ~13 psu (fig. 29). Like figure 28 shows, the 

steepest gradient in salinity occurs in the southern portion of Swinomish Channel. North 

of the south tripod site the salinity averaged in excess of 20 psu. 

Figure 29. Map of the average spatial salinity gradient along Swinomish Channel based 

on mean surface water salinities measured at all stations in March, May, and July, 2006.

58
Surface Water Transport Times and Temporal Salinity Gradients 

Of concern to juvenile Chinook use of the Swinomish Channel is the influence of the 

high current velocities on fresh water mixing, salinity gradients, and transport time to the 

high salinity water of Padilla Bay if and when entrained by the high current velocities as 

fry. Habitat restoration aimed at reconnecting the migratory fish pathways through 

McGlinn Island and a source of fresh water to maintain suitable salinity gradients for fry 

Chinook migration (figs. 2 and 3) will benefit from the net northward current flow in the 

Swinomish Channel. High northward current velocities will also impact the rate at which 

juvenile Chinook are transported to and through the high-salinity waters of Padilla Bay 

en route to important refuge and rearing habitat in the nearshore eelgrass meadows there. 

High northward current velocities will also influence the degree and extent of freshwater 

mixing beyond restored connections to the North Fork Skagit River. 

Given the record of circulation during the deployment (fig. 30A), we calculated the total 

transport (fig. 30B) and travel time of surface water and passive particles over the 11-km 

distance between McGlinn Island and Padilla Bay (fig. 30C). These calculations are 

based on transport observed at the south tripod site. Variations likely exist along channel, 

however, similar transport at the north tripod site and across-channel (fig. 23) support 

these conclusions. 

 

Figure 30. (A) Surface-water velocities during the deployment with positive current 

velocities to the north, negative velocities to the south. (B) Net transport based on 

instantaneous surface current velocities. (C) Surface-water travel between McGlinn 

Island and Padilla Bay (11 km). 

59
Water, passive particles, and/or juvenile fish entrained by current velocities exceeding 

their swimming capacity, can be advected the length of the Swinomish Channel (11 km) 

in as little as 2.1 hours (fig. 30C); the maximum transit time was 6 days. Figure 31 shows 

a histogram of the percent of time that transport occurred along the 11-km distance from 

McGlinn Island to Padilla Bay in 6-hour intervals during our study. The mean transport 

time was ~1 day while the mode, the most frequent transport duration, was 3.75 hours. 

Transport within the mode time of 3.75 hours occurred 17 percent of the time. Critical to 

juvenile and fry Chinook survival are the salinity gradients encountered while smolting 

during outmigration. Although a mean spatial salinity gradient of 13 psu exists in surface 

waters between Padilla Bay and McGlinn Island (fig. 29), during strong northward 

transport this gradient varies significantly in time because of the large magnitude and 

variation in current velocities and relatively persistent mixed salinity regime north of the 

Rainbow Bridge (figs. 27, 28, and 29). During periods of strong northward transport, 

juvenile (fry) Chinook entrained in high current velocities can be advected through these 

salinity regimes in as little as 2.1 hours, within 3.75 hours 17 percent of the time, and 

within 1 day 50 percent of the time. Under these transport rates, they can experience a 

temporal salinity gradient exceeding 4 psu per hour (fig. 31). The temporal salinity 

gradient calculated for the mode transport rate is ~3 psu per hour, whereas the temporal 

salinity gradient associated with the mean transport rate observed is ~0.5 psu per hour. 

Figure 31. Distribution of surface-water travel times between McGlinn Island 

and Padilla Bay binned at 6-hour intervals and associated temporal salinity gradient that 

exists in Swinomish Channel in terms of practical salinity units of change per hour. 

60
This information provides important constraints on determining the volume of 

freshwater needed to support suitable salinity gradients for migrating juvenile salmon. 

They will also help to guide design and placement of refuge habitats along the 

Swinomish Channel that can provide suitable salinity and adequate time for smolt given 

the rapid transport of water between southern Swinomish Channel and the high salinity 

waters of Padilla Bay. These results raise important questions including how do 

circulation processes during other climate (seasonal, interannual) and fluvial conditions 

modify the patterns we observed, how persistent are zones of mixing along Swinomish 

Channel and what are the processes responsible, and how will addition of freshwater 

modify the processes operating today. 

Conclusions 

Under the current circulation regime of the Swinomish Channel, suitable low-salinity 

(<15-20 psu) surface waters for fry Chinook salmon (Healey, 1991) are largely restricted 

to the area between the southern region near the North Fork Skagit River jetty fish 

passage and Hole in the Wall. Periodically, but for short duration, surface water lenses 

with salinity as low as 15 psu extended to the Rainbow Bridge during high river 

discharge and peak flood-tidal currents between March and July, 2006. Generally, 

however, the mean change in surface-water salinity between McGlinn Island and Padilla 

Bay during this time was 10-13 psu, with salinities >20 psu between the town of La 

Conner and Padilla Bay. Currents in the Swinomish Channel during the 2006 spring 

outmigration of Skagit River Chinook ranged 0 to 1.2 m/s and were generally higher in 

the upper 1 m surface waters. Net transport was to the north, toward Padilla Bay. 

Transport times for surface water to travel the 11 km from the southern end of 

Swinomish Channel at McGlinn Island to Padilla Bay ranged from 2.1 hours to 5.5 days. 

The mean travel time was ~1 day, whereas 17 percent of the time, transport of water and 

passive particles occurred within 3.75 hours. The high overall salinities of the channel 

restrict suitable habitat for pre-smolt Chinook salmon to the southern Swinomish 

Channel. 

High northward current velocities have the capacity to transport Chinook fry into less 

suitable, high-salinity waters between Rainbow Bridge and Padilla Bay within hours. The 

rapid transport times of 2.1 to 3.75 hours between McGlinn Island and Padilla Bay which 

occur 17 percent of the time, are considerably less than the time considered adequate for 

juvenile Chinook to acclimate (Healey, 1991). Rapid transport times under the current 

salinity regime produce a temporal salinity gradient that exceeds 4 psu/hour during high 

northward current flow. Although, lower current velocities likely afford more suitable 

conditions along the channel edges, repeat across-channel measurements showed that 

flow was uniformly high across the entire channel at McGlinn Island Causeway. 

Therefore, refuge habitats along Swinomish Channel that provide escape from large and 

abrupt changes in salinity and the high current velocities may be beneficial to juvenile 

salmonids. In addition, increased supply of freshwater sources along this important 

salmon migratory pathway probably would be valuable. Important questions raised by 

this study include how circulation processes during other climate (seasonal, interannual) 

61
wind and fluvial conditions operate and modify the patterns and mixing zones observed. 

It will also be important to determine how additions of freshwater will modify the 

processes operating today. 

Acknowledgments 

We thank Steve Hinton, Eric Beamer, Greg Hood, and Karen Wolf of Skagit River 

System Cooperative and Todd Mitchell and Sarah Akin of the Water Resources Team of 

the Swinomish Indian Tribal Community Office of Planning and Community 

Development for their logistical support and fruitful discussions. We thank Eric Beamer, 

Greg Hood, and Reg Reisenbichler (U.S. Geological Survey) for insight and review of 

biologically sensitive material regarding salinity effects on juvenile salmon. Funding for 

this study was provided by the Skagit River System Cooperative through a grant from the 

Washington State Salmon Recovery Funding Board, the U.S. Geological Survey Coastal 

and Marine Geology Program and the U.S. Geological Survey Multidisciplinary Studies 

of Coastal Habitats in Puget Sound (CHIPS) Project. 

References Cited 

Beamer, E., Bernard, R., Hayman, B., Hebner, B., Hinton, S., Hood, G., Kraemer, C., 

McBride, A., Musslewhite, J., Smith, D., Wasserman, L., and Wyman, K., 2005, Skagit 

Chinook recovery plan. http://www.skagitcoop.org/ 

Collins, B., 2000, Mid-19th century stream channels and wetlands interpreted from 

archival sources for three north Puget sound estuaries—Report to Skagit River System 

Cooperative. 65 p. [http://www.skagitcoop.org/EB1474_Collinspercent202000.PDF]. 

Healey, M.,1991, Life history of Chinook salmon, in Groot, C., and Margolis, L., (eds.), 

Pacific salmon life histories: Vancouver, British Columbia, UBC Press, p. 311-393. 

Oberg K.A., Morlock, S.E., and Caldwell, W.S., 2005, Quality-assurance plan for 

discharge measurements using acoustic doppler current profilers: U.S. Geological 

Survey Scientific Investigations Report 2005-5183, 46 p. 

[http://pubs.usgs.gov/sir/2005/5183/SIR_2005-5183.pdf]. 

Pawlowicz, R., Beardsley, B., and Lentz, S., 2002, Classical tidal harmonic analysis 

including error estimates in MATLAB using T_TIDE: Computers and Geosciences, v. 

28, p. 929-937. 

Yates, S., 2001, Effects of Swinomish Channel jetty and causeway on outmigrating 

Chinook salmon (Oncorhynchus tshawytscha) from the Skagit River, Washington: 

Bellingham, Western Washington University, Master’s thesis, 65 p. 

62
Appendixes 

Appendix I. Conductivity, Temperature, Depth Profiles from U.S. 

Geological Survey Cruise Activity K-2-06-PS. 

The following pages show individual plots of salinity and temperature with depth for the 

stations listed in the accompanying table collected during U.S. Geological Survey Cruise 

Activity K-2-06-PS. 

K-2-06-PS Conductivity, Temperature, Depth Measurement Log 

FILENAME SITE LON LAT UTC_DATETIME 

K206ps_001 F_Dock -122.49691 48.39502 3/28/2006 16:30:14 

K206ps_003 Hole_in_wall -122.50857 48.37675 3/28/2006 20:55:04 

K206ps_004 - -122.50750 48.44428 3/28/2006 22:30:46 

K206ps_005 Mooring -122.50137 48.38721 3/29/2006 0:15:43 

K206ps_006 F_dock -122.49682 48.39519 3/29/2006 16:32:27 

K206ps_007 Mooring -122.50108 48.38703 3/29/2006 16:49:21 

K206ps_008 TRP_South -122.50880 48.37672 3/29/2006 17:01:52 

K206ps_009 2B -122.51037 48.37508 3/29/2006 17:11:49 

K206ps_010 2A -122.51080 48.37551 3/29/2006 17:19:06 

K206ps_011 3B -122.50912 48.37177 3/29/2006 17:24:13 

K206ps_012 4B -122.51546 48.36983 3/29/2006 17:30:00 

K206ps_013 GreenMrkr15 -122.52218 48.36879 3/29/2006 17:34:43 

K206ps_014 GreenMrkr13 -122.53013 48.36712 3/29/2006 17:41:43 

K206ps_015 GreenMrkr11 -122.53854 48.36516 3/29/2006 17:46:43 

K206ps_016 GreenMrkr5 -122.55064 48.36255 3/29/2006 17:53:27 

K206ps_017 - -122.55789 48.35996 3/29/2006 17:59:12 

K206ps_018 - -122.55673 48.35693 3/29/2006 18:06:33 

K206ps_019 - -122.55941 48.36403 3/29/2006 18:16:28 

K206ps_020 3B -122.50930 48.37247 3/29/2006 18:45:48 

K206ps_021 2B -122.51010 48.37561 3/29/2006 18:57:17 

K206ps_022 TRP_south -122.50918 48.37631 3/29/2006 19:00:56 

K206ps_023 1B -122.50782 48.37871 3/29/2006 19:06:57 

K206ps_024 5B -122.50717 48.38234 3/29/2006 19:15:13 

K206ps_025 6B -122.50189 48.38729 3/29/2006 19:24:13 

K206ps_026 7B -122.49740 48.39296 3/29/2006 19:34:12 

K206ps_027 F_Dock -122.49688 48.39531 3/29/2006 19:47:13 

K206ps_028 F_Dock -122.49689 48.39529 3/29/2006 22:11:12 

K206ps_029 NSWIN_N_RR_bridge -122.51534 48.45912 3/29/2006 22:56:12 

K206ps_030 Tripod_N -122.50783 48.44446 3/29/2006 23:13:28 

K206ps_031 11B -122.50011 48.43499 3/29/2006 23:28:36 

K206ps_032 10B -122.50146 48.42645 3/29/2006 23:37:54 

K206ps_033 9B -122.49756 48.41323 3/29/2006 23:50:42 

K206ps_034 8B -122.49690 48.40216 3/30/2006 0:04:24 

K206ps_035 7B -122.49806 48.39370 3/30/2006 0:19:40 

63
K206ps_036 6B_Mooring -122.50105 48.38751 3/30/2006 0:30:03 

K206ps_037 5B_ShelterCove -122.50708 48.38258 3/30/2006 0:39:52 

K206ps_038 1B -122.50787 48.37911 3/30/2006 0:47:26 

K206ps_039 TRP_S -122.50958 48.37579 3/30/2006 0:54:56 

K206ps_040 3B -122.50940 48.37270 3/30/2006 1:00:45 

K206ps_041 Near_fish_passage (FP) -122.50903 48.37130 3/30/2006 1:05:48 

K206ps_042 3B -122.50861 48.37257 3/30/2006 1:11:46 

K206ps_043 2C -122.50924 48.37570 3/30/2006 1:19:17 

K206ps_044 2A -122.51041 48.37591 3/30/2006 1:25:38 

K206ps_045 Mooring -122.50119 48.38719 3/30/2006 1:35:52 

K206ps_046 F_Dock -122.49687 48.39532 3/30/2006 1:51:45 

K206ps_047 F_Dock_am -122.49687 48.39532 3/30/2006 16:03:36 

K206ps_048 TRP_S -122.50838 48.37665 3/30/2006 16:37:52 

K206ps_049 3B -122.50942 48.37223 3/30/2006 16:45:11 

K206ps_050 mid_chan_FP -122.50918 48.37190 3/30/2006 16:50:31 

K206ps_051 FP -122.50949 48.37140 3/30/2006 16:55:50 

K206ps_052 center_chan -122.51031 48.37111 3/30/2006 17:03:00 

K206ps_053 near_Eagle_house -122.51123 48.37089 3/30/2006 17:10:06 

K206ps_054 Mrkr16 -122.51060 48.37049 3/30/2006 17:15:06 

K206ps_055 South_side_chan -122.50987 48.37068 3/30/2006 17:20:56 

K206ps_056 South_chan_FP -122.50957 48.37101 3/30/2006 17:28:46 

K206ps_057 South_side -122.50914 48.37162 3/30/2006 17:34:32 

K206ps_058 McGlinn_Isl_Causeway -122.50867 48.37225 3/30/2006 17:40:26 

K206ps_059 3B -122.50936 48.37219 3/30/2006 17:44:41 

K206ps_060 wall_edge_3C -122.50918 48.37391 3/30/2006 17:50:46 

K206ps_061 2B -122.51025 48.37540 3/30/2006 17:59:11 

K206ps_062 2C -122.50930 48.37532 3/30/2006 18:03:56 

K206ps_063 TRP_S -122.50852 48.37678 3/30/2006 18:08:46 

K206ps_064 Mooring -122.50127 48.38712 3/30/2006 18:20:32 

K206ps_065 F_dock_late_am -122.49687 48.39532 3/30/2006 18:33:56 

64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
Appendix II. Conductivity, Temperature, Depth Profiles from U.S. 

Geological Survey Cruise Activity K-3-06-PS. 

The following pages show individual plots of salinity and temperature with depth for the 

stations listed in the accompanying table collected during U.S. Geological Survey Cruise 

Activity K-3-06-PS. 

K-3-06-PS Conductivity, Temperature, Depth Measurement Log 

FILENAME SITE LON LAT UTC_DATETIME 

k306ps_001 TRP_south -122.50825 48.37711 5/14/2002 22:02 

k306ps_002 G_Dock -122.49643 48.39930 5/14/2002 22:44 

k306ps_003 G_Dock -122.49642 48.39925 5/15/2002 17:01 

k306ps_004 Mooring_site -122.50121 48.38692 5/15/2002 17:49 

k306ps_005 TRP_north -122.50772 48.44436 5/15/2002 18:34 

k306ps_006 Tripod_SBS -122.54442 48.34714 5/15/2002 22:35 

k306ps_007 Tripod_SBN -122.55787 48.36850 5/15/2002 23:12 

k306ps_008 G_Dock -122.49644 48.39926 5/16/2002 16:30 

k306ps_009 Mooring_Site -122.50115 48.38716 5/16/2002 17:41 

k306ps_010 3B -122.50935 48.37193 5/16/2002 18:03 

k306ps_011 TRP_south -122.50839 48.37689 5/16/2002 18:10 

k306ps_012 Shelter_Bay -122.50708 48.38200 5/16/2002 18:17 

k306ps_013 Near53_Karluk -122.49754 48.39159 5/16/2002 18:29 

k306ps_014 G_Dock -122.49643 48.39924 5/16/2002 18:41 

81
82
83
84
85
Appendix III. Conductivity, Temperature, Depth Profiles from U.S. 

Geological Survey Cruise Activity K-4-06-PS. 

The following pages show individual plots of salinity and temperature with depth for the 

stations listed in the accompanying table collected during U.S. Geological Survey Cruise 

Activity K-4-06-PS. 

K-4-06-PS Conductivity, Temperature, Depth Measurement Log 

FILENAME SITE LON LAT UTC_DATETIME 

k406ps_001 F_dock -122.49687 48.39486 7/26/2006 15:54 

k406ps_002 Bridge -122.50171 48.38706 7/26/2006 16:12 

k406ps_003 Shelter_Bay -122.50707 48.38234 7/26/2006 16:22 

k406ps_004 TRS -122.50868 48.37667 7/26/2006 16:30 

k406ps_005 5B -122.51010 48.37462 7/26/2006 16:36 

k406ps_006 3B -122.50920 48.37236 7/26/2006 16:41 

k406ps_007 60 -122.51043 48.37098 7/26/2006 16:52 

k406ps_008 4B -122.51548 48.37009 7/26/2006 16:58 

k406ps_009 offshoreSBS -122.54440 48.34676 7/26/2006 17:45 

k406ps_010 SBN -122.55781 48.36827 7/26/2006 18:55 

k406ps_011 4B -122.51545 48.36987 7/26/2006 20:24 

k406ps_012 60 -122.51028 48.37107 7/26/2006 20:28 

k406ps_013 3B -122.50920 48.37236 7/26/2006 20:45 

k406ps_014 5B -122.51017 48.37458 7/26/2006 20:43 

k406ps_015 TRS -122.50837 48.37690 7/26/2006 20:46 

k406ps_016 Shelter_Bay -122.50696 48.38241 7/26/2006 20:52 

k406ps_017 Bridge -122.50165 48.38733 7/26/2006 20:59 

k406ps_018 F_dock -122.49680 48.39628 7/26/2006 21:18 

86
87
88
89
90
91
Appendix IV. Metadata 

Metadata: 

 Identification_Information: 

 Citation: 

 Citation_Information: 

 Originator: Grossman. E.E., Stevens, A., and Gelfenbaum, G. 

 Publication_Date: 2007 

 Title: 

 Nearshore circulation and water column properties 

 in the Skagit River Delta, Northern Puget Sound, 

 Washington: Tables and profiles 

 Geospatial_Data_Presentation_Form: spreadsheet 

 Larger_Work_Citation: 

 Citation_Information: 

 Originator: Grossman. E.E., Stevens, A., and Gelfenbaum, G. 

 Publication_Date: 2007 

 Title: 

 Nearshore circulation and water column properties 

 in the Skagit River Delta, Northern Puget Sound, Washington 

 Geospatial_Data_Presentation_Form: spreadsheet 

 Series_Information: 

 Series_Name: Scientific Investigations Report 

 Issue_Identification: 2007-5120

 Publication_Information: 

 Publication_Place: Menlo Park, CA 

 Publisher: 

 U.S. Geological Survey, Coastal and Marine Geology Program 

 Online_Linkage: http://pubs.usgs.gov/sir/2007/5120/ 

 Description: 

 Abstract: 

 Nearshore currents, tides, surface water temperature and salinity were 

 measured at two locations continuously and at many discrete stations 

 periodically throughout the Swinomish Channel between March 28 and July 

 26, 2006 to examine circulation, transport and mixing of fresh water 

 along a principal Chinook salmon migratory pathway during their spring 

 outmigration. Results indicate that a significant spatial salinity 

gradient (14 psu) exists between the North Fork Skagit River and 

essential forage habitat in Padilla Bay that likely presents a 

formidable physiological barrier for Chinook smolts. Strong net 

northward current flow in Swinomish Channel driven by semi-diurnal 

tides, results in rapid (3.75-6.00 hr) transport of water and passive 

particles along the 11-km salinity gradient ~20percent of the time. 

Juvenile 

salmonids unable to swim against high currents may experience changes 

in salinity of several parts per thousand each hour during strong 

northward flow. 

 Purpose: 

 These data were collected as part of a Washington State Salmon Recovery 

 Board funded project to examine nearshore circulation in the Swinomish 

 Channel and the feasibility of re-introducing a connection between the 

 North Fork Skagit River and Swinomish Channel for fish passage and 

 Fresh water supply. 

 Time_Period_of_Content: 

 Time_Period_Information: 

 Range_of_Dates/Times: 

 Beginning_Date: 20060328 

 Ending_Date: 20060726 

 Currentness_Reference: ground condition 

 Status: 

 Progress: Complete 

92
 Maintenance_and_Update_Frequency: None planned 

 Spatial_Domain: 

 Bounding_Coordinates: 

 West_Bounding_Coordinate: -122.55941 

 East_Bounding_Coordinate: -122.49642 

 North_Bounding_Coordinate: 48.45912 

 South_Bounding_Coordinate: 48.34676 

 Keywords: 

 Theme: 

 Theme_Keyword_Thesaurus: ISO 19115 Topic Category 

 Theme_Keyword: geoscientificinformation 

 Theme_Keyword: inlandWaters 

 Theme: 

 Theme_Keyword_Thesaurus: none 

 Theme_Keyword: nearshore circulation 

 Theme_Keyword: water column properties 

 Theme_Keyword: conductivity 

 Theme_Keyword: temperature 

 Theme_Keyword: depth 

 Place: 

 Place_Keyword_Thesaurus: General 

 Place_Keyword: Swinomish Channel 

 Place_Keyword: Northern Puget Sound 

 Place: 

 Place_Keyword_Thesaurus: 

 Geographic Names Information System (GNIS) 

 Place_Keyword: Skagit River 

 Place_Keyword: Puget Sound 

 Place_Keyword: Washington 

 Access_Constraints: None 

 Use_Constraints: 

 Public domain data are freely redistributable 

 with proper metadata and source attribution. 

 Please recognize the U.S. Geological Survey (USGS) 

 as the source of this information. 

 Point_of_Contact: 

 Contact_Information: 

 Contact_Organization_Primary: 

 Contact_Organization: U.S. Geological Survey 

 Contact_Person: Eric E. Grossman 

 Contact_Address: 

 Address_Type: mailing and physical address 

 Address: 400 Natural Bridges Dr 

 City: Santa Cruz 

 State_or_Province: CA 

 Postal_Code: 94060-5792 

 Country: USA 

 Contact_Voice_Telephone: (831)427-4725 

 Contact_Facsimile_Telephone: (831)427-4748 

 Contact_Electronic_Mail_Address: egrossman@usgs.gov 

 Browse_Graphic: 

 Browse_Graphic_File_Name: 

 http://walrus.wr.usgs.gov/infobank/k/k206ps/html/k-2-06-ps.nav.html 

 Browse_Graphic_File_Description: 

 Image showing location and extent of K-2-06-PS data. 

 Browse_Graphic_File_Type: GIF 

 Browse_Graphic: 

 Browse_Graphic_File_Name: 

 http://walrus.wr.usgs.gov/infobank/k/k306ps/html/k-3-06-ps.nav.html 

 Browse_Graphic_File_Description: 

 Image showing location and extent of K-3-06-PS data. 

 Browse_Graphic_File_Type: GIF 

 Browse_Graphic: 

93
 Browse_Graphic_File_Name: 

 http://walrus.wr.usgs.gov/infobank/k/k406ps/html/k-4-06-ps.nav.html 

 Browse_Graphic_File_Description: 

 Image showing location and extent of K-4-06-PS data. 

 Browse_Graphic_File_Type: GIF 

 Cross_Reference: 

 Citation_Information: 

 Originator: 

 U.S. Geological Survey, Coastal and Marine Geology Program 

 Publication_Date: 2007 

 Title: InfoBank 

 Online_Linkage: 

 http://walrus.wr.usgs.gov/infobank/k/k206ps/html/k-2-06-ps.meta.html 

 http://walrus.wr.usgs.gov/infobank/k/k306ps/html/k-3-06-ps.meta.html 

 http://walrus.wr.usgs.gov/infobank/k/k406ps/html/k-4-06-ps.meta.html 

 Data_Quality_Information: 

 Logical_Consistency_Report: 

 The time-series measurements of currents and physical water properties 

Were made at two discrete tripod locations, while the surface temperature 

And salinity were made continuously at the Rainbow Bridge only. In 

contrast, individual CTD casts were made over a much broader spatial 

coverage but at discrete points in time and are used to develop a better 

understanding of spatial variability under processes constrained at the 

fixed tripod and mooring locations. 

 Completeness_Report: 

 All data from current, tide, and physical water property measurements 

Were included in analyses after verification and quality control 

procedures were made to ensure that data contained valid clock times and 

station location information. 

 Lineage: 

 Process_Step: 

 Process_Description: 

 Current meter data were quality checked for accurate clock times and 

 non-valid data points (above water) were removed. The east and north 

 components of velocity were rotated to account for the site-specific 

 variation in magnetic declination (17.8 °E), then rotated into along 

 and across- channel components using principle component analysis 

 (PCA). A standard (33-hr) low-pass filter was then applied to the 

 rotated velocities to plot current patterns occurring at subtidal 

 frequencies. Cumulative along-channel transport was calculated by 

 taking the cumulative sum of the product of the along-channel velocity 

 component and Δt. CTD measurements were processed with standard 

 Seabird protocols using Seabird calibrations and correcting for 

 surface soak and instrument priming. Measurements were averaged at 

 0.25-m depth intervals and merged with navigation, environmental data 

 (tide stage, winds, river discharge), and current measurements. Roving 

 ADCP data were processed with WinRiver software following USGS 

 protocols of Oberg et al (2005). 

 Process_Date: 2007 

 Spatial_Data_Organization_Information: 

 Direct_Spatial_Reference_Method: Point 

 Spatial_Reference_Information: 

 Horizontal_Coordinate_System_Definition: 

 Geographic: 

 Latitude_Resolution: 0.00001 

 Longitude_Resolution: 0.00001 

 Geographic_Coordinate_Units: Decimal degrees 

 Vertical_Coordinate_System_Definition: 

 Depth_System_Definition: 

 Depth_Datum_Name: Local surface 

 Depth_Resolution: 0.1 

 Depth_Distance_Units: meters 

 Depth_Encoding_Method: Implicit coordinate 

94
 Entity_and_Attribute_Information: 

 Detailed_Description: 

 Entity_Type: 

 Entity_Type_Label: Filename 

 Entity_Type_Definition: 

 name of water column profile file for a station 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: LocalTime 

 Entity_Type_Definition: 

 month/day/year hour:minute of survey at a station 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: Tide 

 Entity_Type_Definition: 

 tide level in meters (m) for a station 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: TideState 

 Entity_Type_Definition: 

 tide state for a station 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: RiverFlow 

 Entity_Type_Definition: 

 river flow rate in cubic feet per second (cfs) for a station 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: Current 

 Entity_Type_Definition: 

 current velocity in centimeters per second (cm/s) for a station 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: Direction 

 Entity_Type_Definition: 

 direction of the current in degrees (degrees) for a station 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: Depth 

 Entity_Type_Definition: 

 depth in meters (m) for a station or site 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: Salinity 

 Entity_Type_Definition: 

 salinity in practical salinity units (psu) for a station or site 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: FILENAME 

 Entity_Type_Definition: 

 name of CTD log profile file for a site 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: SITE 

 Entity_Type_Definition: 

 name of a site 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: LON 

 Entity_Type_Definition: 

 longitude of CTD tripod at a site 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

95
96

 Entity_Type_Label: LAT 

 Entity_Type_Definition: 

 latitude of CTD tripod at a site 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: UTC_DATETIME 

 Entity_Type_Definition: 

 month/day/year hour:minute of survey at a site 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Entity_Type: 

 Entity_Type_Label: Temperature 

 Entity_Type_Definition: 

 temperature in degrees Centigrade (¡C) for a site 

 Entity_Type_Definition_Source: U.S. Geological Survey 

 Distribution_Information: 

 Distributor: 

 Contact_Information: 

 Contact_Organization_Primary: 

 Contact_Organization: U.S. Geological Survey 

 Contact_Person: Eric E. Grossman 

 Contact_Address: 

 Address_Type: mailing and physical address 

 Address: 400 Natural Bridges Dr 

 City: Santa Cruz 

 State_or_Province: CA 

 Postal_Code: 94060-5792 

 Country: USA 

 Contact_Voice_Telephone: (831)427-4725 

 Contact_Facsimile_Telephone: (831)427-4748 

 Contact_Electronic_Mail_Address: egrossman@usgs.gov 

 Distribution_Liability: 

 Although all data have been used by the USGS, 

 no warranty, expressed or implied, is made by the USGS 

 as to the accuracy of the data and/or related materials. 

 The act of distribution shall not constitute any such warranty, 

 and no responsibility is assumed by the USGS in the use 

 of these data or related materials. 

 

 Any use of trade, product, or firm names is 

 for descriptive purposes only and does not imply 

 endorsement by the U.S. Government. 

 Metadata_Reference_Information: 

 Metadata_Date: 20070515 

 Metadata_Contact: 

 Contact_Information: 

 Contact_Organization_Primary: 

 Contact_Organization: U.S. Geological Survey 

 Contact_Person: Eric E. Grossman 

 Contact_Address: 

 Address_Type: mailing and physical address 

 Address: 400 Natural Bridges Dr 

 City: Santa Cruz 

 State_or_Province: CA 

 Postal_Code: 94060-5792 

 Country: USA 

 Contact_Voice_Telephone: (831)427-4725 

 Contact_Facsimile_Telephone: (831)427-4748 

 Contact_Electronic_Mail_Address: egrossman @usgs.gov 

 Metadata_Standard_Name: 

 FGDC Content Standards for Digital Geospatial Metadata 

 Metadata_Standard_Version: FGDC-STD-001-1998