Seasonality of Boundary Conditions for Cook Inlet, Alaska

Steve Okkonen

Principal Investigator

Co-principal Investigators:

Scott Pegau

Susan Saupe

Final Report

OCS Study MMS 2009-041

August 2009
This study was funded in part by the U.S. Department of the Interior, Minerals Management 

Service (MMS) through Cooperative Agreement No. M08AR12674, originally numbered as 

Cooperative Agreement No. 0102CA85294, Task Order No. 37628, between MMS, Alaska Outer 

Continental Shelf Region, and the University of Alaska Fairbanks. 

The views and conclusions contained in this document are those of the authors and should not be 

interpreted as representing the opinions or policies of the U.S. Government. Mention of trade 

names or commercial products does not constitute their endorsement by the U.S. Government. 
Seasonality of Boundary Conditions for Cook Inlet, Alaska

Steve Okkonen

Principal Investigator

Co-principal Investigators:

Scott Pegau

Susan Saupe

Final Report

OCS Study MMS 2009-041

August 2009
Contact information 

 Coastal Marine Institute 

 School of Fisheries and Ocean Sciences 

 University of Alaska Fairbanks 

 P. O. Box 757220 

 Fairbanks, AK 99775-7220 

 email: sharice@sfos.uaf.edu 

 phone: 907.474.7208 

 fax: 907.474.7204 

 
1

TABLE OF CONTENTS 

List of Figures................................................................................................................................2

List of Appendices.........................................................................................................................5

Abstract..........................................................................................................................................6

Project Organization.....................................................................................................................7

Introduction...................................................................................................................................7

Methods.........................................................................................................................................13

Results...........................................................................................................................................17

Discussion.....................................................................................................................................46

Summary......................................................................................................................................54

Acknowledgements......................................................................................................................54

Study Products.............................................................................................................................55

References....................................................................................................................................56 
2

LIST OF FIGURES 

Figure 1. Each yellow dot represents a sampling station along a transect 

line (circled numbers). Red dots are the locations of moorings 

added as part of this program.....................................................................................9

Figure 2. Sampling stations are shown on the bathymetry......................................................10 

Figure 3. Plots of monthly average wind speed (top) and vector-averaged 

direction (bottom) at the Augustine (solid line) and Drift River 

(dotted line) NDBC C-MAN stations are provided..................................................11

Figure 4. The first panel shows the circulation pattern in lower Cook Inlet 

presented by Burbank (1977) and the second panel is the pattern 

proposed by Muench et al. (1978)............................................................................12

Figure 5. Pictured is the CTD used on most cruises................................................................14

 

Figure 6. River discharge data for the Susitna River in upper Cook Inlet 

is shown....................................................................................................................18 

Figure 7. Plotted are the temperature measurements since 1990 made at the 

Seldovia and Kodiak tide stations.............................................................................19

Figure 8. The plots are the fitted mean salinity (top left), the salinity amplitude 

(top right), the day of the minimum salinity (lower left), and the 

standard error of the fit (lower right) for line 5........................................................21

Figure 9. Fitted salinity data for line 4 is presented with the same order as 

figure 8......................................................................................................................22

 

Figure 10. Fitted salinity data for line 3 is presented with the same order as 

figure 8......................................................................................................................23 

Figure 11. Fitted salinity data for line 2 is presented with the same order as 

figure 8......................................................................................................................24 

Figure 12. Fitted salinity data for line 1 is presented with the same order as 

figure 8......................................................................................................................25

Figure 13. The plots are the fitted mean temperature (top left), the temperature 

amplitude (top right), the day of the maximum temperature (lower 

left), and the standard error of the fit (lower right) for line 5...................................27

Figure 14. Fitted temperature data for line 4 is presented with the same order 

as figure 13...............................................................................................................28 
3

Figure 15. Fitted temperature data for line 3 is presented with the same order 

as figure 13...............................................................................................................29 

Figure 16. Fitted temperature data for line 2 is presented with the same order 

as figure 13...............................................................................................................30

Figure 17. Fitted temperature data for line 1 is presented with the same order 

as figure 13...............................................................................................................31

Figure 18. April salinity (left column) and temperature (right column) contour 

plots are shown.........................................................................................................32

Figure 19. September salinity (left column) and temperature (right column) 

contour plots are shown............................................................................................33 

Figure 20. Minimum geostrophic currents are observed in May...............................................34 

Figure 21. Maximum geostrophic currents are observed in September.....................................35

Figure 22. Freshwater transport by the geostrophic currents across lines 1 

through 4 are provided..............................................................................................36

Figure 23. Water levels at Seldovia during the 2006 spring-neap tide 

measurement sequence are provided with the sampling period 

outline in blue...........................................................................................................36

Figure 24. Salinity contours along line 1 are displayed in the left panel and 

temperature in the right............................................................................................38 

Figure 25. Salinity contours along line 6 (Cape Adams to Cape Douglas) are 

displayed in the left panel and temperature in the right...........................................39 

Figure 26. Salinity contours along line 7 (Magnet Rock to Mt. Augustine) are 

displayed in the left panel and temperature in the right...........................................40 

Figure 27. Salinity contours along line 3 are displayed in the left panel and 

temperature in the right............................................................................................41 

Figure 28. Salinity contours measured during 2005 by the Alaska Department 

of Fish and Game Offshore Test Fisheries program................................................42 

Figure 29. Salinity and depth data collected by a mooring on the eastern shelf 

of Kennedy Entrance is presented...........................................................................44 
4

Figure 30. A short segment of the data presented in figure 29 is presented to 

show the fluctuations in salinity with tide stage.......................................................45 

Figure 31. Salinity contours along lines 1 and 2 are provided in the top panel 

and temperature is in the lower panel.......................................................................48 

Figure 32. Temperature -salinity plots for April along line 1 (Kennedy), line 2 

(Shelikof), line 3 (Anchor), line 4 (Barabara) showing that line 4 

has a different characteristic than the other Cook Inlet waters.................................49 

Figure 33. Sea surface temperature image of Cook Inlet is shown............................................50 

Figure 34. A SeaWiFS chlorophyll image of lower Cook Inlet is shown..................................51 

Figure 35. The inferred surface circulation pattern is shown.....................................................53 
5

LIST OF APPENDICES 

Appendix 1. Station locations.....................................................................................................57

Appendix 2. Cruise dates............................................................................................................59 
6

ABSTRACT 

In order to continue improving our understanding of the physical environment of lower and central Cook 

Inlet, Alaska and to augment recent MMS-funded observational and modeling efforts we monitored 

oceanographic conditions that measured the seasonal changes in hydrographic properties at the inflow and 

outflow boundaries in lower Cook Inlet and the northern Gulf of Alaska and investigated the 

mechanism(s) influencing the distributions of these properties. During 2004 to 2006 we collected 

hydrographic measurements along transect lines crossing: 1) Kennedy Entrance and Stevenson Entrance 

from Port Chatham to Shuyak Island; 2) Shelikof Strait from Shuyak Island to Cape Douglas; 3) Cook 

Inlet from Red River to Anchor Point; 4) Kachemak Bay from Barbara Point to Bluff Point, and 5) the 

Forelands from East Foreland to West Foreland. During the third year we added two additional lines; 6) 

Cape Douglas to Cape Adams, and 7) Magnet Rock to Mount Augustine. The sampling in 2006 focused 

on the differences in properties during the spring and neap tide periods. 

Strong seasonal variations in temperature and salinity were observed along all of the transect lines. 

Temperature reflected seasonal changes in solar insolation whereas freshwater content reflected seasonal 

changes in snowmelt, runoff, and precipitation patterns. Seasonal changes in freshwater input through the 

Alaska Coastal Current (ACC) and river discharge into Cook Inlet most likely control the non-tidal 

circulation in the lower portion of Cook Inlet. The freshwater-driven circulation was highly modified by 

the large tides of Cook Inlet. This modification could be seen at all time scales down to the individual 

tide. Tidal mixing near the mouth of Kachemak Bay during spring tides altered the flow of freshwater 

into lower Cook Inlet. The resultant path of the ACC appears to be controlled by the interaction of the 

tides with the bathymetry. 

Previous studies examined seasonal changes at depth using moored instrumentation or looked at 

hydrographic properties over a very limited portion of the year. This study adds to the previous work by 

providing the seasonal changes in hydrographic properties at the surface as well as at depth along several 

transect lines in lower and central Cook Inlet. This work is the first to examine the variability of 

hydrographic properties over a range of temporal cycles (days - seasonal) and provides our first 

understanding of the role of the spring-neap cycle on controlling the distribution of those properties. 

The temperature and salinity gradients between and across lower and central Cook Inlet suggest five 

principal factors necessary for accurate numerical simulations of Cook Inlet hydrography and circulation. 

These conditions include accurate spatial and/or temporal representations of (1) freshwater discharges 

into Cook Inlet (e.g. Susitna River, Matanuska River, Kenai River, and other CI river discharges), (2) heat 

and salt fluxes through Kennedy Entrance (including ACC transport), Stevenson Entrance, Shelikof 

Strait, (3) bathymetry, (4) tidal forcing and (5) solar insolation. Although wind forcing is also an 

important forcing mechanism, it was not directly investigated as part of this project, nor its role readily 

discernable from the hydrographic data. 
7

PROJECT ORGANIZATION 

This project was conducted by Steve Okkonen, W. Scott Pegau, and Susan Saupe. There were two main 

geographic portions of this study. The central Cook Inlet study was led by Dr. Okkonen and the lower 

Cook Inlet study was led by Dr. Pegau. Differences of equipment and techniques make separating the 

description of methods by these geographic regions. Within each study area there were ConductivityTemperature-Depth (CTD) hydrographic surveys and moored deployments of a CTD. 

INTRODUCTION 

Cook Inlet is an important water body in Alaska, nearly two thirds of Alaska’s population lives along its 

shores and watershed. Its geology changes dramatically from the upper to the lower portion of the Inlet 

creating a diverse array of habitats and species in its waters. It is home to productive commercial and 

sport fishing activities. It also is the main transportation route for cargo into Alaska. Oil and gas 

exploration and production has occurred in the northern portion of the Inlet since the early 1960’s. The 

management of resources within Cook Inlet requires an understanding of how it functions as a system. 

Cook Inlet is a broad, long, and shallow embayment extending northward from the Gulf of Alaska into 

south-central Alaska (Figures 1 and 2). Several large rivers flow into the northern (upper) section of 

Cook Inlet. Discharges from these rivers have large seasonal variability with high flows associated with 

snowmelt in the spring and storm events in the fall. The bathymetry shoals to less than 100 m near the 

mouth of Cook Inlet. A deeper channel extends along the axis of the Inlet, and has branches into 

Kachemak Bay and around Kalgin Island. The shape and depth of Cook Inlet is such that the M2 tide 

resonates leading to a very large tidal amplitude. The Inlet is narrower towards the north causing the tidal 

amplitude and resulting currents to increase towards the constriction formed by the Forelands. Changes 

in tidal flow associated with the changes in bathymetry forms strong shear and convergence zones locally 

known as rips. These rips accumulate debris, ice, and oil, as was demonstrated in the 1987 T/V Glacier 

Bay oil spill. 

Winds in Cook Inlet are largely driven by the strength and position of the Aleutian Low and the 

mountainous terrain surrounding the Inlet. In the winter the Inlet winds are driven by the cyclonic flow 

around the Aleutian Low (MMS EIS 2003) and generally are from the north and northeast (Figure 3). 

During the summer the Inlet winds are more often from the south and southwest, driven in part by the 

temperature gradient from land to the ocean. Stronger winds form in areas with gaps in the mountains, 

such as in Kamishak Bay where mountains funnel air in a southeast direction through Kamishak Bay and 

across the Barren Islands. Winds weaken in central Cook Inlet. 

Much of our understanding of the circulation of the lower portion of Cook Inlet comes from studies 

conducted in the 1970’s (Burbank 1977, Barrick 1978, Muench et al. 1978, Muench et al. 1981). These 

investigators used hydrographic surveys, current meter moorings, drifters, satellite images, and highfrequency radar to infer the circulation. Most of these studies focused on the spring and summer, with the 

exception of Muench et al. 1981, which looked at summer and winter circulation using moored sensors. 

Although the studies were conducted during a similar time frame, there are significant differences in the 

inferred circulation proposed by Burbank (1977) and Muench et al. (1978). The primary differences in 

the two studies are the path of the ACC and the path of freshwater flowing out of Cook Inlet along the 

western side (Figure. 4). 

Recently a number of studies have been conducted in Cook Inlet. Two workshops have been held that 

produced proceedings that describe the modern research (Johnson and Okkonen 2000, Schumacher 2005) 

which includes a pair of temperature and salinity studies that are precursors to this work (Okkonen and 
8

Howell 2003, Okkonen 2004). Other recent work has focused on the interactions between the physical 

and biological properties (Speckman et al. 2005) and modeling of upper Cook Inlet (Oey et al. 2007). 

During the period of this work there were several other activities to improve our understanding of 

circulation in Cook Inlet. A group led by Mark Johnson from the University of Alaska Fairbanks (UAF) 

released drifters at the northern portion of our study area and worked on improving the 3-dimensional 

models. The National Oceanic and Atmospheric Administration (NOAA) placed several acoustic doppler 

current profiler (ADCP) moorings in the Inlet to improve the tidal current predictions. Alaska Department 

of Fish and Game (ADF&G) began profiling measurements of oceanographic properties in association 

with the offshore test fishery program conducted through July. Both NOAA and UAF investigators 

installed high-frequency radar units to map surface currents. A more complete description of recent 

efforts can be found on the internet 

(http://doc.aoos.org/other_meetings/2005/cook_inlet_physical_oceanography_workshop_proceedingscombined%20sections-final-2006.pdf) which includes the proceedings of a Physical Oceanography of 

Cook Inlet workshop held as part of this project. 

In this work we examine the variability in hydrographic properties at time scales of seasons to days, how 

that variability is forced, and the implications for circulation in the area. The descriptions of oceanic 

properties provided here also provide boundary conditions necessary for numerical circulation models 

currently existing (e.g. CIRCAC and NOAA HAZMAT) and under development (e.g. CMI-funded model 

by Mark Johnson, or the Regional Ocean Model by Alaska Ocean Observing System). 
9

Figure 1. Each yellow dot represents a sampling station along a transect line (circled numbers). 

Red dots are the locations of moorings added as part of this program. The Offshore test fishery 

data comes from the center of line 3. Lines 1, 2, and 5 demark the boundaries of lower and central 

Cook Inlet, with line 3 separating lower and central Cook Inlet. 
10

Figure 2. Sampling stations are shown on the bathymetry. Red bathymetry is shallow and dark 

blue is approximately 200 meters depth. The 100m isobath occurs at the transition from yellow to 

blue. 
11

Figure 3. Plots of monthly average wind speed (top) and vector-averaged direction (bottom) at the 

Augustine (solid line) and Drift River (dotted line) NDBC C-MAN stations are provided. Augustine 

is within Kamishak Bay in lower Cook Inlet and Drift River is in central Cook Inlet. 
12

Figure 4. The first panel shows the circulation pattern in lower Cook Inlet presented by Burbank 

(1977) and the second panel is the pattern proposed by Muench et al. (1978). 

 
13

 

METHODS 

Conductivity-temperature-depth (CTD) hydrographic surveys were conducted along seven transect lines 

(Figure 1 and Appendix 1) in Cook Inlet. Each survey was conducted using a SeaBird Electronics SBE19+ CTD with ancillary sensors (Figure 5). Survey dates and frequency of sampling were different 

between the two regions because of weather and scheduling constraints. The survey dates are provided in 

Appendix 2. 
14

Figure 5. Pictured is the CTD used on most cruises. The rope below goes to a weight that was used 

to reduce flagging in fast current regimes. 

Lower Cook Inlet Hydrographic Surveys

The CTD surveys were conducted six times in 2004 and 2005, and four times in 2006. In 2004 and 2005 

only lines 1 through 4 were occupied. In 2006 lines 6 and 7 were added in lower Cook Inlet to determine 

the location where the ACC crosses Cook Inlet. Line 5 survey characteristics are described below in the 

Central Cook Inlet Hydrographic Surveys section. In 2003 we focused on the spring and summer season 

with cruises in April, May, June, July, August, and September. In 2004 we included fall and winter with 

surveys in January, April, June, July, September, and October. We tried to conduct surveys during neap 

tides when possible to allow the CTD to reach greater depths. The exact date of each cruise was primarily 

dictated by having a period of two days where the expected wind speed was 15 knots or less and seas less 

than seven feet. These conditions were desired for safety in deploying the equipment from the smaller 

(~50 foot) vessels that were used. In 2006 we scheduled surveys to occur in the fall to coincide with high 

freshwater discharge. The cruises were scheduled during spring and neap tides to examine the role of the 

fortnightly tides on the distribution of hydrographic properties. It took just under two days to complete 
15

lines 1 through 4, and an additional day to add lines 6 and 7. Depending on the weather, surveys were 

initiated on either line 1 or 3 and ended on line 4. 

The survey lines were designed with stations spaced one nautical mile (nm) apart close to each shore and 

two nm apart farther offshore (Figure 2, Appendix 1). Line 1 crossed Kennedy and Stevenson Entrances, 

passing between the Barren Islands midway along the line. Line 1 consisted of 22 stations. Line 2 

consisted of 16 stations across Shelikof Strait. Line 3 ran just north of the confluence of Cook Inlet and 

Kachemak Bay between the Anchor and Johnson Rivers. Line 4 had 10 stations spaced one nm apart 

between Barabara and Bluff Points in Kachemak Bay. Line 6 included 27 stations extending across the 

mouth of Cook Inlet between Cape Adams and Cape Douglas. Lastly, line 7 had 24 stations extending 

between Magnet Rock and Augustine Island. The water depth along this line averages approximately 75 

meters, considerably less than the depth along line 6. 

The SBE-19+ CTD and ancillary sensors were placed in a cage and a 5 -10 Kg weight on a 1-m long line 

was hung beneath the cage (Figure 5). The purpose of the weight was to help reduce the flagging of the 

cage in the strong currents and to provide an indication when the cage neared the bottom. At each station 

the CTD was started and allowed to soak a couple meters below the surface for one minute before starting 

a profile. The CTD was lowered at approximately 0.5 m s-1 until it hit the bottom or the line was 

completely let out (200 m). The CTD was retrieved at one m s-1 or faster. 

The data were downloaded at the end of each sampling trip and processed using standard SeaBird 

processing algorithms. The data were first run through Datcnv to apply the calibration coefficients. The 

Filter algorithm was applied using manufacturer recommended filter constants. Plumbing lags were 

applied using Alignctd. The lags were determined each year by examining up and downcasts and getting 

them to align. Alignment was also constrained by preventing salinity and density spikes in the final data 

set. The Loopedit algorithm was applied to only keep data when the sensor was descending. The salinity, 

density, and depth were then calculated using the Derive algorithm. The data were then binned into 1-m 

depth bins using only the downcast data and the Binavg algorithm and then output in an ASCII tabular 

format. 

All of the ASCII data from a given cruise were combined into a single spreadsheet and the cruise number, 

station number, date, time, latitude, longitude, and station depth were added to the data from each station. 

These cruise data sheets were then used in the plotting and analysis of the data, and were submitted the 

National Ocean Data Center and to the Alaska Ocean Observing System for inclusion in their databases. 

Lower Cook Inlet Mooring 

The southern mooring consisted of a SeaBird Microcat CTD recorder mounted on the top of a 2X2 m crab 

pot that had the webbing stripped off. The mooring was placed on the shelf just west of Kennedy 

Entrance (59° 12.161N 151° 50.860W). The mooring location was chosen to avoid the strong currents 

in Kennedy Entrance and the need to protect the mooring from storms. The mooring was deployed on 

August 12, 2006 and retrieved on October 28, 2006. The instrument was retrieved to prevent damage by 

the strong winter storms that occur in the area. The Microcat was programmed to collect an average five 

samples every 15 minutes. The raw data were collected in Alaska Standard Time and then converted to 

UTC. 

While this program did not have a mooring component that covers the entire sampling period, it is 

important to have some measure of the interannual variability. One source of oceanographic data is from 

the NOAA tide stations in Kodiak and Seldovia, which are just outside of the study region. The data can 

be found on the NOAA website. 
16

(http://tidesandcurrents.noaa.gov/station_retrieve.shtml?type=Meteorological%20Observations) The sixminute water temperature data were averaged to provide a monthly water temperature record. 

Central Cook Inlet Hydrographic Surveys 

A Sea-Bird Electronics, Inc. SBE 19+ Profiler CTD was used to acquire surface-to-bottom measurements 

of temperature and salinity during surveys along an east-west transect (latitude 60° 43’N) between the 

East Foreland and West Foreland (line 5) in central Cook Inlet, Alaska (Figure 1). Five surveys were 

conducted along this transect between May and October in 2004 and four surveys were conducted from 

May to October in 2005. These surveys generally occurred during mid-to-late stages of the flood tide 

(predominantly northward-flowing surface currents). Two additional surveys were conducted on 9 August 

2006 to compare hydrography across the Forelands transect during flood and ebb. The survey dates are 

listed in Appendix 2. 

Sampling along each crossing of the 14.5-km (~8 nm) Forelands transect generally took a little less than 

1.5 hours. Successive CTD casts were separated by 2 minutes of longitude (~1.81 km; ~1 nm). Cast 

locations were acquired from a vessel-mounted GPS unit. The CTD was lowered at approximately 0.5 m 

s

-1 and individual measurements of temperature, salinity, and pressure were acquired at a rate of four per 

second. Temperature, salinity, and density (sigma-t) data from each downcast were averaged in 1-m bins 

centered on integer depths. 

Central Cook Inlet Mooring 

A Sea-Bird Electronics, Inc. SBE 37-SM microcat CTD was deployed on a bracket attached to the leg of 

the XTO ‘C’ platform in central Cook Inlet (60° 45.7’N, 151° 30.3’W) on 11 August 2006 to acquire time 

series measurements of near-surface temperature and salinity. The XTO platform lies 5 km north of the 

Forelands transect. Subsequent inspection of the bracket on 28 August 2006 showed that the bracket had 

become loose and the microcat was removed. Data were collected every 15 minutes during the 

deployment. 

Further processing 

To determine the seasonal changes each depth bin (z) of the CTD data from each station (x) of the 16-

cruise time series were fit using least squares to the sinusoidal function 

F(x,z,t) = A·cos (2π·t/365) + B·sin (2π·t/365) + C·t + D 

from which two-year mean temperatures, salinities, and densities at each CTD station and integer depth 

were calculated according to 

F(x,z) = ΔT

F(x, z,t) t

t 730

t 0

∫

=

=

d

. 

In this formulation, t = 0 corresponds to 1 January 2004. The amplitudes and phases of the annual period 

temperature, salinity, and density signals at each CTD station and integer depth were determined from the 

corresponding least squares coefficients, where amplitude = (A2

 + B2)

1/2 , and phase = tan-1(B/A). 
17

Surface geostrophic currents were estimated from the hydrographic transects. This was accomplished by 

calculating geopotential anomalies (or dynamic heights, (ΔΦA )) at location (A) using: 

ΔΦA = ∫

2A

1A

P

P

δdp

where δ is the specific volume anomaly, which is integrated between pressure surfaces.  The

surface velocity is estimated from the slope of the ocean surface calculated using:  

L

ΔΦ ΔΦ

f

1

v B − A =

where v is the velocity perpendicular to the transect line, f is the coriolis parameter, and L is the distance 

between points A and B. We assumed a level of no motion at 100 m for our calculations. 

Freshwater content was determined using a mixing model, 

ref

meas

fw S

S F =1− , where Ffw is the fraction of 

freshwater, Smeas is the measured salinity, Sref is the reference salinity, and the salinity of freshwater is 

assumed to be zero. We used 33.8 PSU as the reference salinity to be consistent with Weingartner et al. 

2005. Combining the fraction of freshwater with the volume of water in a 1 meter wide section along the 

area of the transect we estimated the total freshwater in that volume.

Freshwater flux was estimated using the calculated geostrophic currents combined with the freshwater 

content estimates. 

RESULTS 

To provide a measure of inter-annual variability we examined the river discharge into upper Cook Inlet 

and water temperature data from the NOAA tide stations in Kodiak and Seldovia, which are just outside 

of the study region. 

Freshwater input is important in determining the circulation within Cook Inlet. Unfortunately, only a few 

of the rivers are gauged for measuring discharge, and those measurements are not possible when the river 

is covered with ice. Discharge measurements on the Susitna River, the largest draining into upper Cook 

Inlet, shows a maximum discharge in May as the river first opens up (Figure 6, data from 

http://waterdata.usgs.gov/ak/nwis/rt). Through the summer there is considerable variability in the 

discharge associated with rainfall within the drainage basin, but in general the flow decreases from June 

through August and sometime in September it is dramatically reduced as snowmelt ceases and 

precipitation starts to be snow once again. This is in stark contrast to the more coastal areas where 

freshwater input is at its maximum in September and October due to the fall storms (Royer, 1982). 

The water temperature records show large seasonal and interannual variability (Figure 7). During the 

three years of sampling, similar temperatures were observed in 2004 and 2006. The summer of 2005, 

however; was the warmest on record at the Seldovia tide station and the third warmest in Kodiak. The 

seasonal temperature pattern is that the winter cold period lasts from December until March. Beginning 

at the end of March the temperature increases steadily through June. July through September is the 

warmest season and fall storms begin to bring down the temperature in October. The temperature drop in 
18

the fall is dependent on storm activity so it tends to drop rapidly during these events, unlike the steady 

increase in temperature through the spring. 

Figure 6. River discharge data for the Susitna River in upper Cook Inlet is shown. The red line is 

the measured discharge, and the blue line is the estimated discharge. Note that measured values 

are typically from the beginning of May to the end of September. 
19

Figure 7. Plotted are the temperature measurements since 1990 made at the Seldovia and Kodiak 

tide stations. 
20

Mean conditions and seasonal variability of salinity 

The seasonal cycles (mean, amplitude, phase, and standard error) of salinity along transect lines 1-5, as 

estimated using the least squares procedure described above, are summarized in Figures 8-12. 

Comparison of mean salinities from lines 1-5 broadly affirms the known north-south salinity gradient. 

Most of the largest rivers of the Cook Inlet watershed discharge to the Inlet north of the Forelands. 

Consequently, the lowest mean salinities (~26-28) and the largest amplitude seasonal salinity signal (~3) 

within the study occur between the Forelands (line 5; because CTD casts conducted during the March 

2005 Forelands survey only went to ~30 m, least squares estimates were not computed for depths deeper 

than ~30 m). Mean salinities increase from west to east indicating a mean southward baroclinic flow in 

the upper part of the water column. The phase plot indicates that the highest salinities at the Forelands 

occur in mid-February when river discharge is low, while the lowest salinities occur six months later in 

mid-August, roughly coinciding with the middle of the summer discharge pulse (Figure 6). 

About 100 km south of the Forelands, line 3 mean salinities range between ~29 and <31.5. The west-toeast inclination of isohalines on the western side of line 3 indicates mean southward baroclinic flow. The 

single isohaline contour on the eastern side of line 3 and its east-to-west inclination indicate a 

comparatively weaker northward (up inlet) mean flow on the eastern side of Cook Inlet. The salinity 

amplitude is >1 in the upper ~20 m on the west side of the Inlet and ~0.5 on the eastern side of the Inlet. 

The lowest salinities occur in September. 

At line 2, roughly 120 km south of line 3, mean near-surface salinities are < 30.5 along the western side 

of the line and >31 along the eastern side of the line. The broad west-to-east inclination of the mean 

isohalines indicates that the mean baroclinic flow is directed southward, out of the Inlet into Shelikof 

Strait. The seasonal salinity amplitudes in the upper 20 m are ~0.7-1.2 on the west side of Shelikof Strait 

and ~0.5-1.1 on the eastern side of the strait. The lowest salinities occur in late September. The reader 

should note that, at depths greater than about 30 m, the standard errors of the least squares salinity 

estimates are comparable to the corresponding estimated amplitudes of the seasonal signal. This suggests 

that, given the relatively few surveys conducted, the phase estimates for the seasonal salinity signal at 

depths below 30 m are not reliable. 

Mean salinities along line 1 are generally < 31.5 in the upper 20-m of the water column. The ventilation 

of the 31.5 isohaline near the midpoint and near the southern end of line 1 reflects enhanced (likely tidalrelated) mixing in the vicinity of the Barren Islands and Shuyak Island, respectively. Salinities less than 

31 at the northern end of line 1 reveal the presence of the ACC. Broadly speaking, the north-to-south 

inclination of the line 1 mean isohalines indicates westward baroclinic geostrophic flow (into lower Cook 

Inlet). The maximum salinity amplitude along line 1 (~0.8-1.2) occurs in the upper 20 m at the northern 

end of the line, coincident with the mean location of the ACC. Consistent with mooring-based 

measurements acquired near Seward (Weingartner et al., 2005), the phase plot indicates the lowest 

salinities occur late September-early October when ACC surface salinities are lowest. As was the case for 

line 2, phase estimates are not reliable at depths greater than ~30 m because standard errors are 

comparable to the corresponding estimated amplitudes of the seasonal signal. 

Mean salinities along line 4 vary little (31.5-31.0) over most of the water column. The slope of the 

isohalines along line 4 indicate mean eastward baroclinic flow into Kachemak Bay near the southern end 

of the line and mean westward flow out of Kachemak Bay near the northern end of the line. The 

amplitude plot indicates that seasonal amplitudes are ~0.4-0.6 at depths >10 m for most locations. 

However, amplitudes markedly increase to > 1 in the upper 10 m along the northern half of the line. The 

phase plot indicates that this relatively fresh lens is most pronounced in September. 
21

Figure 8. The plots are the fitted mean salinity (top left), the salinity amplitude (top right), the day 

of the minimum salinity (lower left), and the standard error of the fit (lower right) for line 5. 
22

Figure 9. Fitted salinity data for line 4 is presented with the same order as figure 8. 
23

Figure 10. Fitted salinity data for line 3 is presented with the same order as figure 8. 
24

Figure 11. Fitted salinity data for line 2 is presented with the same order as figure 8. 
25

Figure 12. Fitted salinity data for line 1 is presented with the same order as figure 8.
26

Mean conditions and seasonal variability of temperature 

The seasonal cycles (mean, amplitude, phase, and standard error) of temperature along transect lines 1-5, 

as estimated using the least squares procedure, are summarized in Figures 13-17. Due to the large tidal 

range and shallow bathymetry of the upper Inlet, upper Inlet waters warm rapidly in late spring-early 

summer and cool rapidly during the autumn months. Because the lower Inlet waters are directly 

influenced by communication with northern Gulf of Alaska waters, lower Inlet temperatures are warmer 

in the mean and exhibit less seasonal variability than in the upper Inlet. 

The lowest mean temperatures (~5-5.5°C) and the largest amplitude seasonal temperature signal (~8.5°C) 

within the study occur between the Forelands. The alert reader will note that the resulting least squares 

estimate of the temperature minimum is about –3°C. For the observed salinities such an ocean 

temperature is a physical impossibility and, as such, suggests that the limited number of surveys 

contributes to the unrealistic quantitative estimate. The associated phase plot indicates that the maximum 

temperature occurs in mid-August. 

Mean temperatures along line 3 vary little, ranging from ~6.5°C on the west side of the line to ~7°C on 

the east side of the line. Amplitude of the seasonal signal, while less than that near the Forelands, is 

relatively large (~6°C) on the west side compared to the amplitude (~4°C) on the east side. The 

temperature maximum occurs in late August. 

Mean temperatures along line 2 show more thermal stratification than is evident on lines 3 and 5. The 

coolest temperature (~6.5°C) occurs at the western side of the line within a few kilometers of the coast. 

Temperatures >7.5°C characterize the rest of the surface layer. The amplitude of the seasonal signal in the 

surface layer is ~6°C near the western side of the line and ~4.5°C over the remainder of the line. The 

amplitude falls to ~1°C at depths of 80-100 m. The temperature maximum in the upper 100 m of the 

water column occurs in late August-early September. Note that the standard error becomes comparable to 

the amplitude of the seasonal signal at depths below ~100 m. This is much deeper than the ~30 m 

threshold depth for salinity estimates. This difference likely reflects the comparative ease with which heat 

is transmitted through the water column compared to salt (mass). 

The warmest mean temperature (~8°C) on line 1 occurs in association with ACC surface waters near the 

northern end of the line. The ventilation of the 7.5°C isotherm suggests enhanced tidal mixing. The 

amplitude of the seasonal temperature signal is ~4°C in the core of the ACC. The amplitude is less than 

1°C near the bottom between Shuyak Island and the Barren Islands. The warmest temperatures occur in 

September. 

Mean temperatures along line 4 range from ~6.5°C near the bottom to ~7.5°C near the surface. The 

amplitude of the seasonal temperature signal is <3.5°C over most of the water column and is ~4°C near 

the surface. Maximum temperatures near the surface occur in late August and in mid-September at depth. 
27

Figure 13. The plots are the fitted mean temperature (top left), the temperature amplitude (top 

right), the day of the maximum temperature (lower left), and the standard error of the fit (lower 

right) for line 5. 
28

Figure 14. Fitted temperature data for line 4 is presented with the same order as figure 13. 
29

Figure 15. Fitted temperature data for line 3 is presented with the same order as figure 13. 
30

Figure 16. Fitted temperature data for line 2 is presented with the same order as figure 13. 
31

Figure 17. Fitted temperature data for line 1 is presented with the same order as figure 13. 
32

Salinity and temperature measurements representative of spring conditions (seasonally high salinity and 

low temperature) along lines 1-4 are shown in Figure 18. Corresponding measurements representative of 

late summer conditions (seasonally low salinity and high temperature) are shown in Figure 19. In the 

spring, the waters along each line are generally well mixed. In May, increased solar heating and 

freshwater inputs begin to promote stratification that intensifies through September. 

Figure 18. April salinity (left column) and temperature (right column) contour plots are shown. 

Starting at the top the plots represent lines 1 through 4 in order. 
33

Figure 19. September salinity (left column) and temperature (right column) contour plots are 

shown. Starting at the top the plots represent lines 1 through 4 in order. 

While seasonal cycles of temperature and salinity effect seasonal changes in the density field, spatial 

gradients in the density field result in baroclinic geostrophic currents. Geostrophic surface currents 

estimated from the density field show mean flows at a minimum in May and at maximum in September 

and October (Figures 20 and 21). In May, the estimated geostrophic currents are less than 0.2 m/s. They 

rise to over 1.0 m/s in the Western Cook Inlet (WCI) waters and 0.8 m/s in the ACC entering Cook Inlet. 

The strongest currents are in narrow bands in the fronts associated with the WCI waters and the ACC. 

Since freshwater inputs promote intensification of geostrophic currents, the seasonal evolution in 

freshwater transport is similar to the seasonal evolution of geostrophic currents (Figure 22). There is little 
34

freshwater flowing through Kennedy Entrance from January to May. Freshwater transport then builds 

through October. Along line 3 there is a net southward freshwater transport in January that decreases 

until April, after which it increases through October. Southward freshwater transport through Shelikof 

Strait has a minimum in May and reaches a maximum in August. 

Figure 20. Minimum geostrophic currents are observed in May. The scale arrow in the lower left 

represents 50 cm/s. 
35

Figure 21. Maximum geostrophic currents are observed in September. The scale arrow in the 

lower left represents 50 cm/s. 
36

Figure 22. Freshwater transport by the geostrophic currents across lines 1 through 4 are provided. 

Negative transport is out of the box defined by the four lines. Line 1 is dotted, 2 is dashed, 3 is 

dash-dot, and 4 is three dots and a dash. 

The seasonal patterns in oceanographic conditions are modified by forcing at shorter time scales. Cruises 

were conducted during spring and neap tides during the fall of 2006 to examine how circulation in lower 

Cook Inlet changed over the fortnightly tidal cycle. The three dates shown here are July 27th (spring tide), 

August 6th (neap tide), and August 13th (spring tide). Water levels in Seldovia during the sampling 

periods are provided in Figure 23. 

Figure 23. Water levels in meters at Seldovia during the 2006 spring-neap tide measurement 

sequence are provided with the sampling period outline in blue. 
37

A few characteristics of the conditions along line 1 were observed to change. The ACC is evident during 

all three sampling periods (Figure 24), but the salinity decreases within the ACC as time progressed. 

During spring tides in Kennedy Entrance, more saline waters push onto the eastern shelf, altering the base 

of the ACC. The temperature of the deep water increases, and salinity decreases during spring tides. The 

temperature of the ACC was highest during the neap tide when mixing with deep water is minimized. 

Tidal mixing at the Barren Islands creates a colder, more saline water mass around the islands. The width 

of the cold water mass was greatest during spring tides. During the neap tide, a colder, saltier water mass 

is seen at the bottom of Stevenson Entrance. The temperature data suggests that this water mass spills 

into Kennedy Entrance around the Barren Islands. 

Strong winds combined with the large spring tides made conditions too rough to sample in Shelikof Strait 

on the two spring tides of this sequence. Therefore, we were unable to observe changes in Shelikof Strait 

as a function of the strength of the tide. 

Line 6 was placed directly across the mouth of Cook Inlet between Cape Adams in the east and Cape 

Douglas in the west. Line 6 had similarities to the patterns observed along line 1 (Figure 25) in that the 

salinity of the ACC decreased and the WCI salinity increased. At the same time, the bottom had an 

increasing presence of a colder, saltier water mass throughout the measurement sequence. It typically 

took about 30 hours from when we started sampling in Kennedy Entrance until we returned to Cape 

Adams along line 6. This temporal difference can help explain some of the differences observed along 

the eastern portions of lines 1 and 6. 

We observed an increase in surface salinity during the spring tides along line 6. During spring tides, the 

core of the ACC waters remains less than 50 m deep, whereas during neap tide the ACC can be observed 

down to 100m. The deep portion also detached from the shore. During the spring tide there is a salt 

wedge in the center of Cook Inlet that separates the freshwater flowing into and out of Cook Inlet. On the 

neap tide the freshwater plume is observed across the entire mouth of Cook Inlet. 

More dramatic changes between the spring and neap tide conditions can be seen a little further into Cook 

Inlet along line 7 (Magnet Rock to Augustine Island, Figure 26). A freshening of the surface waters is 

observed along the western boundary. The greatest difference between the spring and neap tides occurs 

in the center of the transect and along the bottom. On a spring tide there are two colder, more saline 

parcels of water along the bottom separated by a warmer, fresher water mass in the center. The salinity of 

the western tongue of salty water decreased through the final sampling in September. During the neap 

tide the cold-salty water extends from the bottom to nearly the surface in the center of the transect. 

Further north along line 3 (Anchor Point to Tuxedni Bay) the most obvious difference between the spring 

and neap tide conditions is the extent of WCI water (Figure 27). During a neap tide the typical surface 

salinities are <28 PSU with strong stratification. Fresher water is observed along the eastern side of the 

channel. During the spring tide the salinity of the WCI water is approximately 30 PSU and the 

stratification is reduced. 

Other sources of data are useful in observing the effects of the spring-neap cycle on the water properties 

of Cook Inlet. The Alaska Department of Fish and Game has been monitoring oceanographic conditions 

in the channel portion of line 3 for several years. They make daily transects, and some of the salinity data 

from 2005 can be seen in Figure 28. During the neap tides (1-5, 15-19, 29-31 July), stratification 

increases and surface salinities decrease in the WCI waters. As the tidal amplitude increases into the 

spring phase (7-13 and 21-27 July), the WCI becomes mixed throughout the water column resulting in a 

thicker, more saline water mass. The amplitude of the fortnightly salinity signal of the WCI water mass is 

~1.5. 
38

Figure 24. Salinity contours along line 1 are displayed in the left panel and temperature in the 

right. The data in the panels are from July 27 (spring tide), August 6 (neap tide) and August 13 

(spring tide) as viewed from top to bottom. 
39

Figure 25. Salinity contours along line 6 (Cape Adams to Cape Douglas) are displayed in the left 

panel and temperature in the right. The data in the panels are from July 27, August 6 and August 

13 as viewed from top to bottom. 
40

Figure 26. Salinity contours along line 7 (Magnet Rock to Mt. Augustine) are displayed in the left 

panel and temperature in the right. The data in the panels are from July 27, August 6 and August 

13 as viewed from top to bottom. 
41

Figure 27. Salinity contours along line 3 are displayed in the left panel and temperature in the 

right. The data in the panels are from July 27, August 6 and August 13 as viewed from top to 

bottom. 
42

Figure 28. Salinity contours measured during 2005 by the Alaska Department of Fish and Game 

Offshore Test Fisheries program. The number in the corner is the day in July that the data was 

collected. 
43

Another illustration of fortnightly changes in water properties is provided by data from the mooring 

deployed in August 2006 along the eastern shelf of Kennedy Entrance (Figure 29). During spring tides 

the salinity along the bottom of the shelf increases consistent with that presented in Figure 24. During 

neap tides, salinity decreases as the strength of the ACC increases. The amplitude of the fortnightly 

salinity signal is ~1 at the mooring location. Large fluctuations in salinity are also observed during the 

semidiurnal tide cycle (Figure 30). A representative amplitude of the semidiurnal salinity signal is about 

0.5. Although not shown here, a representative amplitude of the near surface semidiurnal salinity signal at 

the XTO platform was ~1.2. At both mooring sites, the amplitudes of the semidiurnal salinity signals 

were somewhat larger during spring tides than during neap tides. 
44

Figure 29. Salinity and depth data collected by a mooring on the eastern shelf of Kennedy 

Entrance is presented. 
45

Figure 30. A short segment of the data presented in figure 29 is presented to show the fluctuations 

in salinity with tide stage. 
46

DISCUSSION 

Variability in oceanographic conditions occurs at time scales of minutes to decades. The tide station 

temperature data records show the Pacific Decadal Oscillation and shorter term climatic shifts that are on 

the order of five to eight years in duration. Seasonally there is a fairly consistent pattern in the 

oceanographic temperature. Starting in March the water begins to warm at a fairly constant pace until 

July. There is a small peak in temperature in August, but the temperature is fairly steady between July 

and September. Beginning in October there is a rapid decrease until December. The temperatures then 

remain low through March. 

Surface temperatures on the western side of Cook Inlet were observed to go through the largest 

temperature fluctuations. Surface waters along the west side of Cook Inlet originate in the upper Inlet 

where the very shallow depths promote efficient cooling in winter and heating in summer. While the 

western side of Cook Inlet had the most extreme temperature changes, the seasonal cycle was observed 

throughout lower Cook Inlet waters. The one exception to this pattern occurred in the deepest waters of 

Shelikof Strait. In the bottom of Shelikof Strait a cold-saline water mass moved in during the summers 

causing some of the lowest temperatures at the bottom to occur during the summer. This intrusion of 

more saline waters is consistent with the salinity signal observed along the Gulf of Alaska line as 

described by Royer (2005). 

Seasonal changes in the freshwater inputs drive seasonal changes to the salinity field of the Cook Inlet 

region. There are two principal sources of freshwater to the study area, river discharge into upper Cook 

Inlet and ACC transport into lower Cook Inlet. A typical seasonal river discharge profile somewhat 

resembles a step function. Following the winter discharge minimum, river discharge increases by more 

than an order of magnitude during May. Discharge remains high through the summer, though variable, 

and decreases from late September through November. While freshwater is carried into lower Cook Inlet 

throughout the year by the ACC, the freshwater signal varies with seasonal changes in coastal 

precipitation and wind mixing. The resulting ACC salinity minimum occurs in late September-early 

October; about a month later than the salinity minimum occurs in central Cook Inlet 

The seasonal variability in temperature and salinity sets up the hydrographic conditions that drive the 

currents in lower Cook Inlet. There are several potential problems with the geostrophic currents 

estimated from the hydrographic measurements. These include: strength of the tidal currents may inhibit 

the ability to reach geostrophic balance, the spacing between stations being short, current estimates are 

only for the portion perpendicular to the transect line, and assuming a level of no motion forcing the 

solution to provide only the baroclinic portion of the current. The errors in the estimated currents are then 

reflected in the freshwater (FW) transport estimates, which show a net positive FW transport into the 

survey area (Figure 22), which implies an increase in mass within the region. While these calculated 

currents have their limitations, when combined with other sources of information we can begin to provide 

a better picture of circulation in the region. 

It is possible to make some inferences about the flow in lower Cook Inlet using the freshwater content 

estimates. The freshwater content observed along lines 6 and 7 was greater than the amount flowing 

through Kennedy Entrance and south past line 3. The amount of freshwater was greatest along line 6 due 

to the transect line being aligned with the direction of flow, implying that the ACC is crossing Cook Inlet 

near this line. 

After subtracting the southward flowing freshwater observed on line 3, the freshwater content along line 7 

was typically around 65% of that seen along line 6. This result was independent of the spring-neap tide 

cycle. Only on the neap cycle is there a clear pulse of ACC water traveling northward past line 7 and into 

Kachemak Bay. During spring tides, wedges of saltier water are observed near the bottom on each side of 
47

the Inlet with a fresher water section between them. This fresher section is most likely the northern edge 

of the ACC. Anecdotal evidence for this inference was the significant amount of debris, particularly 

fucus and free-floating bull kelp, which signified the presence of a front. 

The fresher water flowing out of lower Cook Inlet appears to be restricted to a band approximately 5 -9 

km wide as it passes Cape Douglas (Figures 1 and 25). This narrow outflow contains most of the 

freshwater flowing south along the west side of Cook Inlet and the ACC waters flowing into Cook Inlet. 

In every one of our observations along line 6 the cross-sectional area of the freshwater band flowing out 

of Cook was smaller than the cross-sectional area of the ACC flowing into Cook Inlet at Cape Adams. 

For example, in Figure 25, the area of water entering with salinity less than 31.5 PSU is three times the 

area of equivalent salinity exiting Cook Inlet. This may be in part due to a stretching of the apparent area 

of the ACC caused by the transect line being at an angle to the direction of flow. A slightly smaller area 

of the ACC is observed along line 1, which has approximately the same starting location, but cuts across 

the ACC at a different angle. Even this smaller area observed along line 1 is double that seen passing 

Cape Douglas in Figure 25, and the water flowing pass Cape Douglas includes the ACC and WCI waters. 

This implies that the outflow past Cape Douglas must be much more rapid than the inflow in order to 

conserve mass. However, the geostrophic baroclinic current estimates don’t reflect the existence of an 

intensified current along the western side of Cook Inlet. As a consequence, the baroclinic freshwater 

transports into and out of the lower Inlet do not sum to zero. 

Mixing of ACC, WCI, and other Cook Inlet waters can be limited by the spring-neap tidal cycle. Figure 

31 shows the WCI water cocooned within the ACC waters as they both flow into Shelikof Strait. A nearsurface (< 15 m) lower salinity lens of WCI water is imbedded in a slightly higher salinity lens of ACC 

water at the northern end of Shelikof Strait. The origins of the two water masses are more evident in the 

temperature data where the imbedded lower-salinity water is at a colder temperature than the ACC water 

flowing into the lower Inlet through Kennedy Entrance and out through Shelikof Strait. We speculate that 

this phenomenon occurs only during periods of weak tidal mixing (neap tide) and high freshwater input. 

Further into Cook Inlet, there is also evidence that tidal mixing may block the exchange of waters 

between areas. The temperature-salinity properties of the deep water in Kachemak Bay are not consistent 

with the properties of water flowing into Cook Inlet through Kennedy Entrance (Figure 32). We 

hypothesize that, during spring when the stratification is relatively weak and more conducive to the 

mixing of the water column, saltier waters form at the confluence of Cook Inlet and Kachemak Bay, even 

during the neap tide. This would restrict exchange of water between Kachemak Bay and Cook Inlet, 

which would account for the differences in the temperature-salinity characteristics between the two water 

bodies. As stratification increases during the summer months, the blocking water only forms during 

spring tides when tidal mixing is relatively strong. During neap tides when tidal mixing is weak, 

exchange between Kachemak Bay and Cook Inlet is enhanced. 

The mixing of the colder-saltier water is also evident in the sea-surface temperature imagery (Figure 33) 

and ocean color imagery (Figure 34). This colder water is bounded on the west by the freshwater flowing 

down Cook Inlet, to the east by warmer water in Kachemak Bay, and to the south by the ACC. Fresher 

water to the west and east suggests that the colder water will follow a cyclonic (counter-clockwise) path. 
48

Figure 31. Salinity contours along lines 1 and 2 are provided in the top panel and temperature is in 

the lower panel. The data presented is from October 2005 and shows the WCI water imbedded in 

the ACC as it passes into Shelikof Strait. 
49

Figure 32. Temperature-salinity plots for April along line 1 (Kennedy), line 2 (Shelikof), line 3 

(Anchor), line 4 (Barabara) showing that line 4 has a different characteristic than the other Cook 

Inlet waters. 
50

Figure 33. Sea surface temperature image of Cook Inlet is shown. The image was obtained from 

the Sea-Air-Land-Modeling-Observation-Network website. Note the colder waters at the 

confluence of Kachemak Bay and Cook Inlet, in the Barren Islands, and to the northeast of Shuyak 

and Afognak Islands. 
51

Figure 34. A SeaWiFS chlorophyll image of lower Cook Inlet is shown. Low chlorophyll values 

(green color) are associated with the strong mixing area at the confluence of Cook Inlet and 

Kachemak Bay. 
52

Daily surveys conducted by ADF&G showed the hydrographic structure near Anchor Point to also be 

modulated during the spring-neap tide cycle (Figure 28). Daily surveys conducted through July showed 

that the spring tides break the freshwater stratification, mixing the freshwater throughout the water 

column on the western side of Cook Inlet. During a neap tide when tidal mixing is relatively weak, the 

freshwater plume flowing along the west side of Cook Inlet is able to maintain strong stratification. Were 

these strong winds to persist for a few days, the stratification would likely weaken somewhat. 

The hydrography of Cook Inlet varies with the semidiurnal tidal cycle, as well as the spring neap cycle. 

The length of the transect lines in lower Cook Inlet were too long to be able to sample fast enough to 

resolve semidiurnal tidal changes. Semidiurnal changes in hydrographic properties are evident in the 

mooring data (Figure 30). During the ebb tide, higher salinity water was carried onto the shelf east of 

Kennedy Entrance. The saltwater flowing onto the eastern shelf would tend to inhibit the flow of the 

ACC into Kennedy Entrance, suggesting there are tidally-driven pulsed intrusions of the ACC into lower 

Cook Inlet. 

In southern Cook Inlet, in the vicinity of the Barren Islands, tidal mixing is observed in the satellite 

imagery and hydrographic samples. The presence of denser water adjacent to the Barren Islands would 

promote counter-clockwise circulation around the islands. This pattern was seen in at least one of the 

drifters deployed by Mark Johnson in his research of circulation in Cook Inlet (Schumacher 2005). 

Remnant tidal flow around the Kodiak Island archipelago is probably the cause of the upwelling seen on 

the northeast side of the archipelago in the satellite imagery, and along the Shuyak end of line 1. 

Upwelling was observed near Shuyak Island on several occasions, even though the winds were very 

weak. The abundance of whales and other marine mammals observed within these upwelling areas are 

indicative of their ecological importance. 

Our results are consistent with the findings of Burbank (1977) and Muench et al. (1978) which depict 

Cook Inlet exhibiting typical estuarine circulation. The dominant freshwater flows are southwestward 

along the western side of Cook Inlet and the ACC flowing westward across the mouth of Cook Inlet 

(Figure 35). Consistent with the findings of Muench et al. (1978, 1981), our results also suggest that the 

core of the ACC tends to follow the 100 m isobaths, 

Data from drifters (http://www.pmel.noaa.gov/foci/FOCI_data.html) and our hydrographic surveys 

suggest that deeper water may intrude further into Cook Inlet than does the ACC. Deep waters from 

Shelikof Strait and Kennedy Entrance appear to be brought to the surface west of the mouth of Kachemak 

Bay as well as intrude north of line 3 along the eastern side of the deep channel. 

Mixing resulting from the interaction of tidal currents at the confluence of Kachemak Bay and Cook Inlet 

may enhance this normal estuarine circulation. The presence of a denser water mass near the mouth of 

Kachemak Bay leads to a single counter-clockwise circulation cell near the mouth of Kachemak Bay. 

It is important to recall that the upper Inlet is fresher than the lower Inlet in all seasons. The south-north 

salinity gradient results from more and larger streams discharging freshwater into the upper Inlet (e.g. 

Mantanuska River, Susitna River) compared to the lower Inlet and from the oceanic influence in the 

lower Inlet. The geostrophic response to the south-north salinity gradient is a westward-flowing, crosschannel baroclinic current. The strength of this cross-channel flow will necessarily vary with seasonal 

changes in river discharge into the Inlet. Based on earlier hydrographic surveys (Okkonen and Howell 

2003) which indicate that the south-north salinity gradient within the study area is strongest between the 

latitudes of Kalgin Island and the Forelands, we infer that the cross-channel baroclinic current should be 

strongest within a few tens of kilometers south of the Forelands. 
53

Figure 35. The inferred surface circulation pattern is shown. The light green lines represent the 

flow of the ACC. The dark blue lines represent the freshwater flowing down from upper Cook 

Inlet. Dashed lines represent weak or intermittent flow paths. The light blue line is freshwater 

leaving Kachemak Bay. The light boxes are areas with persistent upwelling or strong mixing, and 

the red lines are gyres set up in part by the upwelling areas. 
54

SUMMARY 

Changes in solar heating provide a strong seasonal cycle to the oceanographic properties of Cook Inlet. 

More importantly, the seasonal change in freshwater flowing down Cook Inlet, and into Cook Inlet as the 

ACC alter the strength of currents and the exchange of water within the region. The water properties are 

also highly dependent on the tides. Significant mixing, due to the large tides in the area, influences the 

location and strength of salinity gradients and, hence, the location and strength of the geostrophic 

baroclinic currents. The modulation of that mixing during the spring-neap cycle alters the path of the 

ACC and the exchange of water between Cook Inlet and Kachemak Bay. 

Temperature and salinity gradients exist between lower and central Cook Inlet, between the east and west 

sides of the Inlet, and are evident in the hydrographic data acquired through this project. Based on our 

observations we suggest that there are five principal factors necessary for accurate numerical simulations 

of Cook Inlet hydrography and circulation. These conditions include accurate spatial and/or temporal 

representations of (1) freshwater discharges into Cook Inlet (e.g. Susitna River, Matanuska River, Kenai 

River, and other Cook Inlet river discharges, plus precipitation), (2) heat and salt fluxes through Kennedy 

Entrance (including ACC transport), Stevenson Entrance, Shelikof Strait, (3) bathymetry, (4) tidal forcing 

and (5) solar insolation. Although wind forcing is also an important forcing mechanism, it was not 

directly investigated as part of this project, nor its role readily discernable from the hydrographic data. 

With respect to numerically modeling circulation in Cook Inlet, the minimum time and space scales to be 

resolved are those associated with the semidiurnal tide (12.4 hr) and the steep bathymetric slopes. This 

implies a maximum time step of an hour or two and a spatial grid of ~100 m or less. 

Several questions remain to be resolved. What is the role of the winds in altering stratification and the 

path of the major currents? How closely does the seasonal freshwater signal along the west side of Cook 

Inlet resemble the ‘step function’ discharge profile characteristic of upper Cook Inlet rivers? What are the 

mixing rates in different areas of Cook Inlet, and what regions have the strongest upwelling? What are 

the circulation patterns in Kamishak Bay? We hope that other measurement programs that are in progress 

or recently completed will help to answer these questions. 

ACKNOWLEDGMENTS 

We thank the Minerals Management Service and the Coastal Marine Institute (University of Alaska 

Fairbanks) for funding this project. We acknowledge the effort of the captains and crews of several 

vessels Rolfy, Kittiwake, Waters, Columbia, Corrina Kay, and Americanus that supported the CTD 

surveys of lower Cook Inlet. A special thanks goes to John Crosbie for help in determining a suitable 

location for the lower Cook Inlet mooring and effort as part of several of the hydrographic surveys. We 

thank Steve Tvenstrup and Eric Huebsch for their help with the hydrographic surveys near the Forelands, 

and Scott Griffith with XTO Energy for deploying a mooring on their platform. 
55

STUDY PRODUCTS 

Pegau, W.S. 2004. Circulation into Kachemak Bay: Does it affect crab populations. Presentation at the 

Interagency Crab Meeting, December 2004, Anchorage, AK 

Okkonen, S. 2005. Hydrography of Central Cook Inlet: August 2003. In: Cook Inlet Physical 

Oceanography Workshop Proceedings, 

(http://doc.aoos.org/other_meetings/2005/cook_inlet_physical_oceanography_workshop_proceed

ings-combined%20sections-final-2006.pdf). J. Schumacher [ed]. 

Pegau, W.S., S. Saupe, S. Okkonen, and M. Willette (S. Pegau presenter). 2005. Hydrography of lower 

Cook Inlet. In: Cook Inlet Physical Oceanography Workshop Proceedings 

(http://doc.aoos.org/other_meetings/2005/cook_inlet_physical_oceanography_workshop_proceed

ings-combined%20sections-final-2006.pdf). J. Schumacher [ed]. 

Pegau, W.S. 2005. Satellite tools for Cook Inlet. In: Cook Inlet Physical Oceanography Workshop 

Proceedings 

(http://doc.aoos.org/other_meetings/2005/cook_inlet_physical_oceanography_workshop_proceed

ings-combined%20sections-final-2006.pdf). J. Schumacher [ed]. 

Pegau, W.S., S. Okkonen, and S. Saupe (S. Pegau presenter). 2006. Seasonality of boundary conditions 

for Cook Inlet, Alaska. Presentation to CMI Annual Research Review, 14 February 2006, 

Fairbanks, AK. 

Pegau, W.S., E. Cokelet, and S. Saupe. 2006. Oceanographic boundary conditions to Cook Inlet. 

Presentation at 2006 Symposium: Marine Science in Alaska, January 22-25, 2006. Anchorage, 

AK. 

Baird, S., and W.S. Pegau. 2006. Water flow into Kachemak Bay: Is it isolated? Poster presented at the 

Ocean Sciences meeting, February 20-24, 2006. Honolulu, HI. 

Pegau, W.S. 2006. What’s new in the bay. Presentation of research being conducted at the Kachemak 

Bay Research Reserve given to Alaska Department of Fish and Game leadership, NERR 

Stewardship Coordinators, and several others. 

Pegau, W.S. 2007. Connecting oceanography and fisheries in the offshore test fishing program. Poster 

presented at the Alaska Marine Science Symposium. January 24, 2007. Anchorage. Alaska. 

Pegau, W.S., S. Okkonen, and S. Saupe (S. Pegau presenter). 2007. Seasonality of boundary conditions 

for Cook Inlet, Alaska. Presentation to CMI Annual Research Review, February 6, 2007, 

Fairbanks, AK. 
56

REFERENCES 

Barrick, D.E. 1978. HF Surface-current mapping radar 1977 Alaskan operations – lower Cook Inlet. In: 

Environmental Assessment of the Alaskan Continental Shelf. Annual Reports. 39pp. 

Burbank, D.C. 1977. Circulation studies in Kachemak Bay and Lower Cook Inlet. In Environmental Studies of 

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pp. 

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57

APPENDICES 

Appendix 1. Station locations 

Line Station Lon (°W) Lat (°N) 

Water 

Depth Line Station Lon (°W) Lat (°N) 

Water 

Depth 

1 1 151.875 59.203 33 3 39 152.567 60.007 24

1 2 151.890 59.190 40 3 40 152.537 59.997 32

1 3 151.905 59.177 38 3 41 152.510 59.987 35

1 4 151.920 59.157 71 3 42 152.482 59.987 33

1 5 151.952 59.122 123 3 43 152.422 59.957 27

1 6 151.983 59.087 199 3 44 152.368 59.938 52

1 7 152.015 59.052 202 3 45 152.308 59.918 112

1 8 152.047 59.020 217 3 46 152.253 59.900 82

1 9 152.078 58.988 125 3 47 152.200 59.880 73

1 10 152.110 58.957 57 3 48 152.145 59.863 52

1 11 152.142 58.925 84 3 49 152.093 59.845 40

1 12 152.167 58.893 73 3 50 152.040 59.827 38

1 13 152.187 58.862 88 3 51 151.987 59.810 35

1 14 152.207 58.830 124 3 52 151.958 59.798 29

1 15 152.227 58.798 121 3 53 151.935 59.790 22

1 16 152.247 58.767 120 3 54 151.905 59.780 14

1 17 152.267 58.735 122 3 55 151.883 59.772 12

1 18 152.287 58.703 123 

1 19 152.298 58.690 89 4 56 151.650 59.492 21

1 20 152.310 58.677 143 4 57 151.650 59.508 102

1 21 152.322 58.663 137 4 58 151.650 59.525 107

1 22 152.333 58.650 103 4 59 151.650 59.542 86

2 23 152.633 58.613 32 4 60 151.650 59.558 76

2 24 152.662 58.623 54 4 61 151.650 59.575 63

2 25 152.685 58.635 94 4 62 151.650 59.592 35

2 26 152.707 58.643 218 4 63 151.650 59.608 29

2 27 152.767 58.665 194 4 64 151.650 59.625 27

2 28 152.817 58.687 164 4 65 151.650 59.492 10

2 29 152.868 58.703 161 

2 30 152.920 58.722 146 

2 31 152.973 58.742 153 

2 32 153.027 58.760 178 

2 33 153.080 58.780 169 

2 34 153.133 58.789 195 

2 35 153.158 58.812 202 

2 36 153.187 58.820 180 

2 37 153.213 58.830 113 

2 38 153.240 58.838 35 
58

Line Station Lon (°W) Lat (°N) 

Water 

Depth 

(m) Line Station Lon (°W) Lat (°N) 

Water 

Depth 

(m) 

5 1c 151.417 60.717 38 7 66 153.302 59.350 28

5 2c 151.450 60.717 24 7 67 153.268 59.348 42

5 3c 151.483 60.717 21 7 68 153.237 59.355 46

5 4c 151.517 60.717 26 7 69 153.172 59.347 50

5 5c 151.550 60.717 29 7 70 153.107 59.343 50

5 6c 151.583 60.717 61 7 71 153.042 59.342 53

5 7c 151.617 60.717 124 7 72 152.977 59.340 56

5 8c 151.650 60.717 29 7 73 152.912 59.338 72

5 9c 151.683 60.717 9 7 74 152.847 59.335 77

 7 75 152.782 59.333 75

6 90 151.925 59.212 36 7 76 152.717 59.332 71

6 91 151.952 59.205 52 7 77 152.652 59.330 72

6 92 151.980 59.197 104 7 78 152.585 59.327 72

6 93 152.007 59.190 106 7 79 152.520 59.325 70

6 94 152.062 59.175 105 7 80 152.455 59.323 71

6 96 152.172 59.147 125 7 81 152.390 59.320 85

6 97 152.227 59.132 132 7 82 152.325 59.318 88

6 98 152.282 59.118 127 7 83 152.260 59.317 82

6 99 152.335 59.103 96 7 84 152.196 59.315 81

6 100 152.390 59.088 113 7 85 152.130 59.313 85

6 101 152.445 59.075 140 7 86 152.097 59.312 76

6 102 152.500 59.060 132 7 87 152.065 59.310 77

6 103 152.555 59.045 138 7 88 152.032 59.310 50

6 104 152.610 59.030 151 7 89 152.000 59.308 27

6 105 152.665 59.017 155 

6 106 152.720 59.002 164 

6 107 152.773 58.988 175 

6 108 152.828 58.973 179 

6 109 152.883 58.958 175 

6 110 152.938 58.945 169 

6 111 152.993 58.930 167 

6 112 153.048 58.915 167 

6 113 153.103 58.902 170 

6 114 153.158 58.887 175 

6 115 153.185 58.880 171 

6 116 153.212 58.872 129 

6 117 153.240 58.865 32 
59

Appendix 2. Cruise dates 

Central Cook Inlet cruises were completed within a few hours. The lower Cook Inlet cruises in 

2004 and 2005 required 48 hours to complete. In 2006 the additions of lines 6 and 7 made it so that 

72 hours were needed to complete the survey. Dates of cruises are the starting date. 

Central Lower 

21-May-04 18-Apr-04 

24-Jun-04 25-May-04 

8-Aug-04 13-Jun-04 

17-Sep-04 17-Jul-04 

9-Oct-04 16-Aug-04 

 7-Sep-04 

 

30-Mar-05 8-Jan-05 

2-May-05 25-Apr-05 

1-Jun-05 14-Jun-05 

26-Aug-05 28-Jul-05 

3-Oct-05 4-Sep-05 

 13-Oct-05 

 

9-Aug-06 26-Jul-06 

 5-Aug-06 

 12-Aug-06 

 11-Sep-06 

 
The Minerals Management Service Mission

As a bureau of the Department of the Interior, the Minerals Management Service’s (MMS) 

primary responsibilities are to manage the mineral resources located on the Nation’s Outer 

Continental Shelf (OCS), collect revenue from the Federal OCS and onshore Federal and 

Indian lands, and distribute those revenues. 

Moreover, in working to meet its responsibilities, the Offshore Minerals Management 

Program administers the OCS competitive leasing program and oversees the safe and 

environmentally sound exploration and production of our Nation’s offshore natural gas, oil and 

other mineral resources. The MMS Royalty Management Program meets its responsibilities 

by ensuring the efficient, timely and accurate collection and disbursement of revenue from 

mineral leasing and production due to Indian tribes and allottees, States and the U.S. Treasury.

The MMS strives to fulfill its responsibilities through the general guiding principals of: (1) being 

responsive to the public’s concerns and interests by maintaining a dialogue with all potentially 

affected parties and (2) carrying out its programs with an emphasis on working to enhance the 

quality of life for all Americans by lending MMS assistance and expertise to economic 

development and environmental protection. 

The Department of the Interior Mission

As the Nation’s principal conservation agency, the Department of the Interior has responsibility 

for most of our nationally owned public lands and natural resources. This includes fostering 

sound use of our land and water resources; protecting our fish, wildlife, and biological diversity; 

preserving the environmental and cultural values of our national parks and historical places; 

and providing for the enjoyment of life through outdoor recreation. The Department assesses 

our energy and mineral resources and works to ensure that their development is in the best 

interests of all our people by encouraging stewardship and citizen participation in their care. 

The Department also has a major responsibility for American Indian reservation communities 

and for people who live in island territories under U.S. administration.