Mention of trade names or commercial products does not constitute endorsement or recommendation 

for their use by the United States government.

Citation for the Full Report

Hartwell, S.I., Apeti, D., Claflin, L.W., Johnson, W.E. and Kimbrough, K. 2011. Sediment Quality Triad 

Assessment in Kachemak Bay: Characterization of Soft Bottom Benthic Habitats and Contaminant 

Bioeffects Assessment. 35pp.
Sediment Quality Triad Assessment in Kachemak Bay: 

Characterization of Soft Bottom 

Benthic Habitats and Contaminant Bioeffects Assessment

S. Ian Hartwell, A. Dennis Apeti, W. Larry Claflin, W. Edward Johnson, and L. Kimani Kimbrough

National Oceanic and Atmospheric Administration

National Ocean Service

National Centers for Coastal Ocean Science

Center for Coastal Monitoring and Assessment

Silver Spring, MD

2011
Table of Contents

LIST OF TABLES....................................................................... i

LIST OF FIGURES.................................................................... i

LIST OF ACRONYMS ............................................................... ii

EXECUTIVE SUMMARY........................................................... iv

INTRODUCTION....................................................................... 1

KACHEMAK BAY STUDY ......................................................... 2

METHODS ........................................................................ 4

RESULTS AND DISCUSSION .................................................. 9

SUPPLEMENTAL SAMPLES AT PORT GRAHAM ................... 23

CONCLUSION ........................................................................ 28

ACKNOWLEDGEMENTS.......................................................... 28

LITERATURE CITED................................................................. 29

List of Tables

Table 1. Number of metals and groups of organic contaminants measured in this study. For 

simplicity the term metal is used without distinction between true metals and metalloids ................6

Table 2. Metal concentration ranges in Kachemak Bay sediments. Values are minimum 

and maximum with the stratum median in parenthesis (μg /g dry weight). Values for Al, 

Si and Fe are expressed in percentage.*Denotes metal concentration above the ERL

values of sediment quality guideline in, at least one site in the study area .......................................12

Table 3. Total number of taxa and abundance per square meter for stations in 

Kachemak Bay nodes........................................................................................................................22

List of Figures

Figure 1. Map of Kachemak Bay study area in Alaska.......................................................................5

Figure 2. Map detailing Lower Cook Inlet and Kachemak Bay circulation pattern .............................5

Figure 3. Top: Map of Kachemak Bay showing sediment collection sites in Kachemak Bay. The inserts 

depict sites within Homer Harbor. Bottom: Map of Kachemak Bay showing sites collected in the Port 

Graham area. The inserts depict sites within Port Graham. .............................................................7
Figure 4. Combined cluster analysis overlays of species clusters and site clusters. The top 

figure illustrates the dominant species communities found in different site clusters. The 

lower figure illustrates how different species assemblages distribute themselves between 

different habitats. ..............................................................................................................................8

Figure 5. Top: Kachemak Bay habitat characterization. Bathymetry with 10 meter 

isobath contours (KBNERR, 2001). Bottom: Water clarity from Secchi disc 

measurements. The water column was significantly more turbid in the east of the bay....................10

Figure 6. Top: Spatial distribution of fine sediment (percent silt + clay). Bottom: total organic 

carbon in sediment at Kachemak Bay study sites, bottom................................................................11

Figure 7. Mean normalized concentrations for trace metals in Kachemak Bay sediments 

(site concentration of each metal and organic class was divided by the overall mean of 

the metal). EF4 is eastern flat station #4...........................................................................................13

Figure 8. Selected metals sediment concentrations from the present study and averaged 

Mussel Watch data from southern Alaska. (Homer = Homer spit; GOA = Gulf of Alaska; 

PWS = average of 5 sites in Prince William Sound)..........................................................................14

Figure 9. Plots of chromium, cadmium, mercury, selenium, lead, copper, nickel and 

zinc (mg/kg) as a function of aluminum concentration in Kachemak Bay sediments. 

Solid triangles - Kachemak Bay; open squares – Homer Harbor. ....................................................15

10

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

Total PCBs ng gm-1

Homer Harbor

Western Subtidal Eastern Flat 

Western Flat

0.2

0.3

0.4

0.5

0.6

0.7

0.8

Total DDTs ng gm-1

Homer Harbor

Eastern Flat 

Western Flat Western Subtidal

2

4

6

8

10

12

Total Butyltins as Sn ng gm-1 

Homer Harbor

Eastern Flat 

Western Flat Western Subtidal

0.2

0.3

0.4

0.5

0.6

0.7

0.8

Total Cyclodienes ng gm-1

Homer Harbor

Eastern Flat 

Western Flat Western Subtidal

0

500

1000

1500

2000

2500

3000

Total PAH W/O Perylene ng gm-1

Homer Harbor

Eastern Flat 

Western Flat Western Subtidal

004

0.06

0.08

0.10

0.12

0.14

0.16

0.18

0.20

Total HCH ng gm-1

Homer Harbor Eastern Flat 

Western Flat Western Subtidal

Figure 10. Mean normalized concentrations for organic contaminants in Kachemak Bay 

sediments (site concentration of each organic class was divided by the overall 

mean of the organic class). ..............................................................................................................16

Figure 11. Concentration of Total PCBs, DDT, and PAHs in sediment from Kachemak Bay 

study sites..........................................................................................................................................17

Figure 12. Top: Concentrations of individual PAHs in sediment from subtidal western sites. Bottom: 

Homer Harbor sites. ..........................................................................................................................19

Figure 13. Grids used for boat hull cleaning and maintenance operations in Homer Harbor. ...........20

Figure 14. Top: Benthic species abundance. Bottom: Benthic species diversity distribution. Strong 

east-west gradients of increasing species abundance and diversity 

were observed...................................................................................................................................21

Figure 15. Benthic species nodal distribution. ..................................................................................23

Figure 16. Top: Eohaustorius estuarius, bioassays demonstrated significant toxicity 

at one station near the Fox River. Bottom: Ampelisca abdita bioassay demonstrated 

significantly reduced survival at one station in Coal Bay ...................................................................24

Figure 17 . Concentrations of individual PAH compounds found at three Port Graham stations. 

The PAH signature for Port Graham appears slightly different from other Kachemak Bay study 

sites, indicative of source differences. Site PG3c resembles Homer Harbor. ...................................25 

i
Figure 18A. Relative concentrations of four elements (cadmium, chromium, mercury, selenium) 

in Kachemak Bay sampling areas and extra sampling stations at Port Graham. 

Concentrations are normalized to the overall mean concentration in the Kachemak Bay only 

(excluding Port Graham) and expressed as a percentage................................................................26 

Figure 18B. Relative concentrations of three elements (arsenic, lead, antimony) in 

Kachemak Bay sampling areas and extra sampling stations at Port Graham. Concentrations are normalized to the overall mean concentration in the Kachemak Bay only 

(excluding Port Graham) and expressed as a percentage................................................................27 

Figure 19. Distribution of ERM quotients in Kachemak Bay, Port Graham, 

and Homer Harbor relative to open water reaches of other bays, and large 

ports around the United States..........................................................................................................28

List of Acronyms

AAS Atomic Absorption Spectroscopy

ADEC Alaska Department of Environmental Conservation

ADF&G Alaska Department of Fish & Game

Ag silver

Al aluminum

AMAP Arctic Monitoring & Assessment Program

AOOS Alaska Ocean Observation System

APHA American Public Health Association

As arsenic

ASTM American Society of Testing and Materials

BT Butyl Tin

Cd cadmium

CFR Code of Federal Regulations

CIRCAC Cook Inlet Regional Citizens Advisory Council

Cr chromium

Cu copper

DDT Dichlorodiphenyltrichloroethane

DO Dissolved Oxygen

EF Eastern Flat

EMAP Environmental Monitoring and Assessment Program

EPA Environmental Protection Agency

ERL Effects Range - Low

ERM Effects Range - Median

ES Eastern Subtidal

EVOS Exxon Valdez Oil Spill

Fe iron

GC/ECD Gas Chromatography/Electron Capture Detector

GC/MS Gas Chromatography/Mass Spectroscopy

gm gram

GOA Gulf of Alaska

H’ Diversity (Shannon-Weiner)

ii
HCH Hexachloro-Cyclohexane

Hg mercury

HH Homer Harbor

HRGS Human Reporter Gene

ICP Inductively Coupled Plasma

KBNERR Kachemak Bay National Estuarine Research Reserve

km kilometer

L Liter

m meter

MDL Method Detection Limit

mg milligram

Mn manganese

MS Matrix Spike

MSD Matrix Spike Duplicate

ng Nanogram

Ni nickel

NIST National Institute of Standards and Technology

NPRB North Pacific Research Board

NOAA National Oceanic and Atmospheric Administration

NS&T National Status and Trends

P Probability

PAH Polycyclic Aromatic Hydrocarbon

Pb Lead

PCA Principal Component Analysis

PCB Polychlorinated Biphenyl

POP Persistent Organic Pollutant

POTW Publically Owned Treatment Plant

ppt parts per thousand

PWSRCAC Prince William Sounds Regional Citizens Advisory Council

QA/QC Quality Assurance/Quality Control

Sb antimony

Se selenium

Si silicon

Sn tin

SQG Sediment Quality Guidelines

SQT Sediment Quality Triad

SRM Standard Reference Material

TBT Tributyltin

TIC Total Inorganic Carbon

TOC Total Organic Carbon

ug microgram

WF Western Flat

WS Western Subtidal

Zn zinc

iii
EXECUTIVE SUMMARY

A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using 

standardized National Status and Trends Bioeffects Program methods. Three sites near the village 

of Port Graham were also sampled for comparison. Concentrations of over 120 organic and metallic 

contaminants were analyzed. Ambient toxicity was assessed using two bioassays. A detailed benthic 

community condition assessment was performed. Habitat parameters (e.g. depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and 

contaminant distribution were also measured at each sampling site. The following is the synopsis of 

findings

• Sediments were mostly mixed silt and sand with pockets of muddy zones. Organic compounds 

(PAHs, DDTs, PCBs, chlorinated pesticides) were detected throughout the bay but at relatively 

low concentrations. With some exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. 

• Homer Harbor had elevated concentrations of metallic and organic contaminants. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in 

the open bay sites. Tributyltin was elevated in Homer Harbor relative to the other areas.

• There was no evidence of residual PAHs attributable to oil spills, outside of local input in the 

confines of the harbor. 

• The benthic community is very diverse. Specific community assemblages were distributed 

based on depth and water clarity. Species richness and diversity was lower in the eastern end 

of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of 

the bay are stressed by the sediment load from glacial meltwater. 

• Significant toxicity was virtually absent. 

• The benthic fauna at Port Graham contained a significant number of species not found in 

Kachemak Bay. 

• Selected metal concentrations were elevated at Port Graham relative to Kachemak Bay, probably due to local geology. Organic contaminants were elevated at a site south of the village. 

iv

(Chugach Wood Carving) 
Sediment Quality Triad Assessment in Kachemak Bay 1 

1. INTRODUCTION 

1.1 National Status and Trends Bioeffects Studies

The National Oceanic and Atmospheric Administration’s (NOAA) National Status and Trends 

(NS&T) Bioeffects Program studies consist of measurement of sediment toxicity, chemistry, and 

benthic community assessment (Sediment Quality Triad - SQT) in estuarine and coastal areas 

throughout the U.S. The NS&T Program has conducted SQT assessment studies in coastal water bodies of the contiguous U.S. and portions of the Hawaiian Islands since 1991. Results from 

previous sediment bioeffects studies in over 20 coastal water bodies and estuaries have been 

published (Long et al. 1996, Turgeon et al. 1998, Long 2000, Hartwell et. al., 2001, Hartwell and 

Hameedi 2007, Harmon et. al., 2003). As a part of the NS&T goal to expand its coastal database to include Alaska, sediment chemistry, toxicity, and benthos assessments were conducted 

in Kachemak Bay. This report presents the results of the study which was funded in part by the 

North Pacific Research Board (NPRB), the Cook Inlet Regional Citizens Advisory Council (CIRCAC), and NOAA. 

1.2 Rationale

Sediment contamination in U.S. coastal area is a major environmental issue because of potential toxic effects on biological resources and often, indirectly, on human health. A large variety 

of contaminants from industrial, agricultural, urban, and maritime activities are associated with 

bottom sediments, including synthetic organic chemicals, polycyclic aromatic hydrocarbons 

(PAHs), and trace elements. Contaminants can biomagnify in the food chain with increasing 

concentration in predatory wildlife and ultimately, in humans. Thus, characterizing and delineating 

areas of sediment contamination and toxicity are viewed as important goals of coastal resource 

management. This is particularly important in Alaska where subsistence food contamination is 

an emerging health concern, especially in rural areas where large amounts of these foods are 

consumed as a primary source of protein (Wolfe 1996). With no known industrial point sources 

of contamination, current sources of pollution to Kachemak Bay may include sewage discharge, 

leaking septic tanks, erosion from metal rich soil, and runoff from old mines. Historically, canneries, mineral, and coal mining in the region have generated shoreline and watershed contaminant 

inputs in the region. Since Kachemak Bay lies between Cook Inlet and Prince William Sound oil 

operations traffic, the possibility of using the bay as shelter for vessels could result in pollution 

from oil leaks and release of other hazardous substance that can impact marine resources. 

1.3 Approach

Bioeffects assessments measure three kinds of parameters; sediment chemistry, sediment animal community condition, and sediment toxicity. These constitute what is referred to as the Sediment Quality Triad (SQT). The SQT is an important ecosystem-based management tool widely 

used by coastal managers for coastal resource management. Study areas are divided into small-
2 Sediment Quality Triad Assessment in Kachemak Bay 

er subunits consisting of uniform habitat type which are sampled at multiple locations. The NS&T 

Bioeffects Program uses a stratified-random statistical design for selection of sampling sites to 

determine the spatial extent of sediment contaminant effects in coastal waters. One of the design principles is to sample all locations in the same time frame and using the exact same methods at all places so that comparison of the severity and spatial extent of impacts between areas 

is possible. 

Chemical contamination assessments include analysis of a large suite of organic compounds, 

pesticides and trace element contaminants. Knowing the concentrations of contaminants in a 

region is critical to understanding where and to what degree pollutants have been released and 

where they accumulate. 

Benthic organisms (animals that live in the bottom sediments) play an important role in the estuarine environment. Critical habitats and food chains supporting many fish, crabs, and wildlife 

species include them. They are composed of diverse species with a variety of life history characteristics. Furthermore, most benthic species have limited mobility and cannot move away from 

stressful environmental conditions. Thus these biological communities are able to integrate the 

complexity of natural stressors and pollutants. Information on changes in benthic populations 

and community patterns due to habitat change can be useful for separating natural variation from 

changes associated with human activities. Benthic community studies have a long history of use 

in regional estuarine monitoring programs and have been proven to serve as an effective indicator for describing the extent and magnitude of pollution impacts and habitat modification in estuarine ecosystems, as well as for assessing the effectiveness of management actions (Llanso et al. 

2004, Long et al. 1995). 

Bioeffects studies also measure toxicity using bioassays (laboratory tests that measure the 

response of animals to sediment that may be contaminated). Sediment toxicity assessments 

are based on a suite of bioassays that assess different levels of effect and exposure. These 

may include direct effects of mortality and/or sub-lethal effects of impaired fertilization, abnormal 

larval development, physiological stress, and biomarkers of exposure to specific chemical contaminants. Tests may be conducted with whole sediment, pore water trapped between sediment 

particles, or extracts from sediments. In this study amphipod mortality bioassays using two species of amphipods were carried out.

2. KACHEMAK BAY STUDY

2.1 Background

Despite its extensive coastline of 33,000 miles, greater than the contiguous US (EPA, 2005), 

and vast natural marine and coastal resources, Alaska lacks adequate data to provide baseline 

information necessary to assess future trends. More environmental monitoring and research is 
Sediment Quality Triad Assessment in Kachemak Bay 3 

needed to assess not only areas of known pollution impact, but also the whole coastal Alaska region. Historically, assessment in the region has been either limited or focused on areas of known 

impairment. 

In collaboration with the U.S. EPA Environmental Monitoring and Assessment Program (EMAP), 

the Alaska Department of Environmental Conservation conducted a region-wide coastal ecological condition study that included assessment of contaminants and benthic communities along 

the Gulf of Alaska and the Aleutian Islands (Saupe et al. 2005). The Cook Inlet Regional Citizens 

Advisory Council (CIRCAC) assesses, water quality, impacts of oil and gas operations, chemical 

and benthic community assessment in Cook Inlet. This NS&T study augments these ongoing efforts to provide detailed data on sediment quality in Kachemak Bay.

2.2 Site Conditions

Kachemak Bay is a 64 km long glacial fjord on the east side of lower Cook Inlet located in south 

central Alaska (Figure 1). At the mouth between Anchor Point in the north and Point Pogibshi to 

the south, Kachemak Bay is nearly 40 km wide but narrows to 10-11 km at Homer Spit which 

cuts the Bay into inner and outer portions (Figure 2). The inner portion of the Bay behind the spit 

is approximately 32 km long. Inner Kachemak Bay is composed of a shallow shelf in the north 

and a deeper zone to the south. The north shore of Kachemak Bay is mostly tidal flats below 

sandy bluffs with numerous coal seams. The south shore has numerous smaller fjords and embayments cut into steep terrain that rises to glaciated valleys and mountain peaks on the Kenai 

Peninsula. Except for the Jakalof Trench running along its southern edge, inner Kachemak Bay 

has a relatively flat bottom and averages 46 m in depth. Glaciers have covered and retreated 

from Kachemak Bay repeatedly over the past 25,000 years. Homer Spit and the Archimandritof 

Shoals to the west of it may be the result of terminal glacial moraines. 

Water circulation in the bay is fueled by the intrusion of saline water from the Gulf of Alaska making the inner bay a fairly saline environment. Freshwater inputs from rivers, glacial meltwater and 

precipitation maintain a slightly brackish water mass with an overall salinity range of 18 – 30‰. 

East of Homer, small canyons cut through the bluff crest, draining the Fritz, McNeil, and Eastland 

Creeks, as well as numerous other creeks toward the head of the Bay. Glaciers on the Kenai 

Peninsula contribute meltwater to the bay during the summer months. The amount of flow from 

glacial rivers can be much higher than from clearwater rivers on the north side. Glacial meltwater 

carries a large sediment load of clay and silt, and this is what gives them their color. The Fox and 

Bradley Rivers in the eastern end of the bay deliver large volumes of freshwater and silt to the 

bay from the Kachemak, Dinglestadt and Chernof Glaciers. which alters water salinity and possibly the water circulation patterns.
4 Sediment Quality Triad Assessment in Kachemak Bay 

Kachemak Bay has a complex water circulation pattern (Burbank 1977, KBNERR 2001). The 

large tides and wind mix the fresh and salty waters that create two circular counterclockwise currents that tend to deposit sediment in the northern portion of the bay (Figure 2). Seasonal winds 

and summer glacial meltwater sometimes causes two currents to merge into one large ring covering the entire bay. This circulation pattern coupled with the tidal exchange help create diverse 

habitats such as tidal flats, kelp beds, marshes and eelgrass north of the relatively deep zone in 

the middle and south portion of the bay. These habitats and the brackish water make the bay an 

excellent spawning ground for several marine organisms (KBNERR 2001).

This nutrient rich estuarine environment sustains a diverse marine wildlife of important economic 

value such as fish, shrimp, crabs, and clams. Additionally, hundreds of plant and animal species inhabit the bay and its watershed, including thriving populations of sea otters, bald eagles, 

moose, black bears, salmon, Pacific halibut and large number of other marine organisms. The 

bay supports significant subsistence and commercial fishery resources and it is considered as 

one of the most productive bays in the U.S. although stocks have been reported to be declining 

in recent years (Szarzi et al. 2007, ADF&G 1998). Commercial harvests of herring, coonstripe 

shrimp, and king, Dungeness, and Tanner crabs have been closed due to depressed stock 

(ADF&G 1998). Other studies point to impacts of natural changes and anthropogenic activities 

that cause pollution as the overriding causes of the depressed stock (Exxon Valdez Oil Spill 

Trustee Council 2002).

2.3 Objectives

The objectives of this project were to:

1)Identify natural and manmade stressors that influence habitat quality and affect benthic community health and distribution; 

2)Provide baseline chemical concentrations for a suite of metals and organic contaminants;

3)Produce a comprehensive species list and distribution patterns of benthic species in soft bottom substrates. 

3. METHODS

The choice of the study location in the northern half of Kachemak Bay was based on the presence of extensive soft bottom habitat, the presence of diverse marine organisms including harvestable species, and water circulation patterns which would likely deliver contaminants or spilled 

oil to a depositional area of the bay. The study site was divided into five areas of relatively uniform habitat: Homer Harbor (HH), intertidal mudflats (WF) and subtidal zones of Coal Bay (WS) 

to a depth of 10 fathoms, and intertidal mudflats (EF) and subtidal zones (ES) east of Coal Bay 

to Chugachik Island. Multiple sampling sites were located on a random basis within each area. 

Three sites were located in Homer Harbor; six sites were located in each area in Coal Bay; and 
Sediment Quality Triad Assessment in Kachemak Bay 5 

Figure 1. Map of Kachemak Bay study area in Alaska

Figure 2. Map detailing Lower Cook Inlet and Kachemak Bay circulation 

pattern.
6 Sediment Quality Triad Assessment in Kachemak Bay 

seven in both of the areas between Coal Bay and Chugachik Island (Figure 3 Top). In addition, 

three sites in the vicinity of the Native Village of Port Graham were sampled to assess that area 

and as a contrast to the Homer area (Figure 3 Bottom). 

3.1. Sampling procedures

Sediment samples were taken at each site in addition to water quality measurements using standard NS&T methods. A total of 29 sites were sampled. The samples were subdivided for distribution to various testing laboratories. Samples were collected for grain size measurement, chemical 

analyses, and toxicity testing. A second sample was taken for benthic community analysis. 

3.2. Chemical analysis

Chemical analyses followed procedures routinely used in the NOAA NS&T Program (Kimbrough 

and Lauenstein 2006a, 2006b, American Society for Testing and Materials [ASTM] 2003). A 

broad suite of sediment contaminants were analyzed at each station, including 55 Polycyclic 

Aromatic Hydrocarbons (PAH) , 18 chlorinated pesticides including DDT and its break-down 

products, 27 Polychlorinated Biphenyls (PCBs), 16 major and trace elements, tributyl-tin and 

its break-down products. Other parameters included grain size (%sand, silt and clay) and total 

organic/inorganic carbon (TOC/TIC). Standard water quality measurements were also collected 

(salinity, dissolved oxygen, clarity, temperature). 

Table 1. Number of metals and groups of organic contaminants measured in this study. For simplicity 

the term metal is used without distinction between true metals and metalloids.

Types of compound Category Number analyzed

Metals and metalloids Elements 16

Butyltins Antifouling pesticide 3

Chlorinated pesticides pesticide 12

DDTs pesticides 6

PAHs Fossil fuel pollutants 55

PCBs Industrial pollutants 27

3.3. Benthic community characterization

All animals were identified to species unless the specimen was a juvenile or damaged. The benthic communities were characterized by abundance (number of animals), number of species, and 

diversity (a type of ratio of abundance and number of species). A special analysis to create a plot 

of the distribution of different communities called a nodal analysis was done. The first step of a 

nodal analysis was to cluster the sites based on the species present at the sites. This step yielded site groups with similar biological communities. The second step was to cluster the species 

based on their presence at the sites. This step yielded species groups with similar habitat types. 

The third step was to plot the results of clustering the sites and species on top of each other in 

a graphical array (Figure 4). In practice, this is done on large 3’x4’ plots of the cluster analysis 

output. Reduction to normal text page size sacrifices a significant amount of detail. 
Sediment Quality Triad Assessment in Kachemak Bay 7 

Figure 3. (Top) Map of Kachemak Bay showing sediment collection sites in 

Kachemak Bay. The inserts depict sites within Homer Harbor. 

(Bottom) Map of Kachemak Bay showing sites collected in the Port Graham 

area. The inserts depict sites within Port Graham.
8 Sediment Quality Triad Assessment in Kachemak Bay 

High abundance

Low abundance 

Species

Sites

Species

Sites High abundance

Low abundance 

Figure 4. Combined cluster analysis overlays of species clusters and 

site clusters. The top figure illustrates the dominant species communities found in different site clusters. The lower figure illustrates how 

different species assemblages distribute themselves between different habitats.

3.4. Sediment toxicity bioassays

Whole sediment mortality bioassays using two species of amphipods (Ampelisca abdita and 

Eohaustorius estuarius) were carried out on the sediment samples. All methods are based on 

standard methods promulgated by the EPA, ASTM, and/or APHA. Results were contrasted to 

physical and chemical characteristics of the sediment on a site-by-site basis. 
Sediment Quality Triad Assessment in Kachemak Bay 9 

4. RESULTS AND DISCUSSION

4.1. Habitat Conditions

• The study area is relatively flat with depth varying from 2.6 – 11.2 m at high tide. Beyond this, 

the bottom falls off more steeply to more than 23 m depth beyond the shelf (Figure 5 Top). Past 

the mouth of the Fox River delta, the shelf drops directly into deep water (greater than 30 m). 

• The water column is fairly well mixed. Only small differences in salinity, temperature and dissolved oxygen (DO) were observed between the surface and bottom. 

• Water clarity showed a distinct gradient from east to west in the bay, reflecting the turbid inflow 

of glacial till transported by the Fox and Bradley Rivers (Figure 5 Bottom)

• Both eastern and western subtidal areas have similar sediment texture of sand to sandy mud. 

• Sediment composition in the intertidal mudflats varied from sandy silt to clayey silt in the eastern 

flat; and from sandy mud to silty sand in the western flat (Figure 6 Top). 

• In the Homer Harbor area, the bottom sediment was mainly composed of fine grained mud. 

• Total organic carbon (TOC) content demonstrated a distinctive gradient between the eastern and 

western areas of the study area (Figure 6 Bottom).

4.2. Chemical Concentrations

4.2.1 Metals

• Concentration and distribution of metals are illustrated in Table 2. In Figure 7, each of the trace 

metal concentrations shown are normalized to the respective mean concentration on a metalby-metal basis. This places the values in the same relative scale and allows for comparison of 

relatively common elements (e.g. zinc) with relatively rare elements (e.g. mercury). 

• In general, trace element concentrations in Homer Harbor were slightly elevated relative to other 

areas. 

• Site EF4 in the eastern flats areas showed spikes in the concentration of silver, chromium, copper, nickel, mercury, selenium, antimony, and zinc 

• Excluding Homer Harbor, metals were found to be significantly elevated in the eastern areas of 

the bay compared to the western areas. 

• Mercury was higher in the western area relative to the eastern areas. 

• Grain size (% fine) was found to be strongly correlated with metals. Metal concentrations are 

elevated in finer grained sediment due to adsorption onto particle surfaces. 

• Most of the trace element concentrations were below sediment quality guidelines known as the 

ERL (Effects range low - concentrations below which toxicity would be expected in less than 

10% of bioassay tests) and ERM (Effects range median – concentrations at which toxicity would 

be expected in 50% of the bioassay tests). Sediment concentrations of arsenic, chromium, copper, and zinc were above the ERL in at least one area. Nickel exceeded the ERM in one site. 
10 Sediment Quality Triad Assessment in Kachemak Bay 

Figure 5. Kachemak Bay habitat characterization. Top: bathymetry with 10 meter isobath contours. 

(KBNERR, 2001). Bottom: water clarity from Secchi disc measurements. The water column was significantly more turbid in the east of the bay.
Sediment Quality Triad Assessment in Kachemak Bay 11 

Figure 6. Top: spatial distribution of fine sediment (percent silt + clay). Bottom: total organic carbon in 

sediment at Kachemak Bay study sites.
12 Sediment Quality Triad Assessment in Kachemak Bay 

Element Homer Harbor Western Flat Western Subtidal Eastern Flat Eastern Subtidal

Ag 0.115 - 0.15 (0.12) 0.08 – 0.112 (0.10) 0 - 0.074 (0.054) 0.07 - 0.14 (0.1) 0.04 - 0.11 (0.07)

As* 14.1 - 17.9 (14.3) 13.7 - 21.4 (17.9) 18 - 48.6 (30.5) 11 – 26 (15) 15 - 43 (20)

Cd 0.19 - 0.22 (0.21) 0.10 - 0.17 (0.15) 0 - 0.10 (0.08) 0.11 - 0.17 (0.12 0 - 0.14 (0.09)

Cr* 94.3 - 96.2 (95.1) 59.3 -73.5 (66.5) 62 - 68 (63) 67.3 – 110 (73.2) 75 – 109 (83)

Cu* 60.2 - 69.4 (64.7) 20.1 - 40.3 (30.4) 22 - 28 (26) 27.5 - 65.6 (34.2) 24 - 40(32)

Hg* 0.11 - 0.12 (0.12) 0.09 - 0.1 (0.1) 0.09 - 0.1 (0.1) 0.06 - 0.10 (0.07) 0.05 - 1.1 (0.1)

Mn 650 – 703 (702) 467 – 635 (502) 500 – 1080 (642) 507 – 863 (567) 592 – 989 (656)

Ni* 45.5 - 45.9 (45.7) 32.0 - 37.7 (35.1) 33.4 - 43.7 (34.5) 34 - 57 (38) 34 - 44 (40)

Pb 13.9 - 14.9 (13.9) 8.29 - 11.6 (9.78) 8.33 - 9.82 (8.70) 9.22 - 15.2 (11.2) 8.56 - 13.6 (11.5)

Sn 1.26 - 1.34 (1.29) 0.93 - 1.33 (1.20) 0.93 - 1.79 (1.10) 1.0 - 2.0 (1.09) 0.9 - 1.8 (1.5)

Se 0.30 - 0.33 (0.3) 0.15 - 0.30 (0.20) 0.0 - 0.27 (0.13) 0.11 - 0.3 (0.2) 0.0 - 0.2 (0.1)

Sn 1.82 - 2.02 (2.01) 1.33 - 1.69 (1.45) 1.13 - 1.72 (1.28) 1.4 - 2 (1.5) 1.5 - 1.8 (1.6)

Zn 144 – 158 (152) 74.5 - 92.6 (82.2) 74 - 83.4 (81.6) 82 – 139 (90) 78 - 97 (91)

Al (%) 7.68– 8.55 (7.69) 6.25 – 7.21 (6.42) 6.6 – 7.2 (7.0) 7.3 – 8.4 (7.6) 6.6 – 7.5 (7.1)

Si (%) 25.7 – 28.8 (25.8) 25.0 – 29.9 (28.3) 27.5 – 32.5 (30.5) 27 – 31 (29) 26.1 – 30.5 (30)

Fe (%) 4.7 – 4.9 ( 4.8) 3.2 – 3.9 (3.6) 3.57 – 6.1 (4.1) 3.3 – 5.3 (3.8) 3.5 – 4.4 (4.2)

Table 2. Metal concentration ranges in Kachemak Bay sediments. Values are minimum and maximum 

with the stratum median in parenthesis (μg /g dry weight). Values for Al, Si and Fe are expressed in 

percentage.*Denotes metal concentration above the ERL values of sediment quality guideline in, at 

least one site in the study area.
Sediment Quality Triad Assessment in Kachemak Bay 13 

0

2

4

6

8

10

12

14

16

18

Normalized Concentration

Ag As Cd Cu Cr Hg Ni Pb Sb Se Zn

Homer Harbor Western Flat Western Subtidal Eastern Flat Eastern Subtidal

EF-4

Figure 7. Mean normalized concentrations for trace metals in Kachemak Bay sediments (site concentration of each metal and organic class was divided by the overall mean of the metal). EF4 is eastern 

flat station #4.

4.2.2 Comparison to other studies

• These results agree with the EMAP findings. Data published by Saupe et al. (2005) also indicated that concentrations of antimony, arsenic, chromium, copper, mercury and zinc were relatively 

elevated in the inner Kachemak Bay. 

• The National Status and Trends Mussel Watch Program has monitoring sites in southeast Alaska 

and the Gulf of Alaska (Kimbrough et al. 2008). Compared to the 1995-1997 Mussel Watch sediment data from Prince William Sound, the concentrations of metals in Kachemak Bay had similar 

ranges with the exception of mercury, which was relatively elevated in Kachemak Bay (Figure 8). 

Mercury concentration, and particularly its biomagnification in aquatic food chain, is a concern 

in Alaska. In Kachemak Bay the source of mercury may be linked to both geological and anthropogenic sources. The Cook Inlet basin that encompasses Kachemak Bay and its watershed lies 

on top of large coal deposits (Flores et al. 2004). Coal has been mined for export and burned for 

electricity in the Homer region. Coal-fired power plants emit mercury, but its presence in Kachemak Bay sediments may be of atmospheric and/or geological source. 

• Cadmium, while high relative to the rest of the system, is nevertheless well below the ERM and 

ERL. Mercury exceeds the ERL, but the high concentration is half of the ERM. Chromium is 

nearly at the ERL level.
14 Sediment Quality Triad Assessment in Kachemak Bay 

0

20

40

60

80

100

120

140

160

180

HH WF WS EF ES Homer Kodiak GOA Skagway Valdez PWS

mg/kg

Chromium

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

HH WF WS EF ES Homer Kodiak GOA Skagway Valdez PWS

mg/kg

Cadmium

0

5

10

15

20

25

30

35

HH WF WS EF ES Homer Kodiak GOA Skagway Valdez PWS

mg/kg

Arsenic

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0.14

HH WF WS EF ES Homer Kodiak GOA Skagway Valdez PWS

mg/kg

Mercury

Figure 8. Selected metals sediment concentrations from the present study and averaged Mussel 

Watch data from southern Alaska. (Homer = Homer spit; GOA = Gulf of Alaska; PWS = average 

of 5 sites in Prince William Sound).

4.2.3 Human versus natural sources

Because all metals have both natural and man-made sources, it is important to identify background metal concentrations in a given study area. To help account for differences in metal 

concentrations among background samples and thereby identify man-made inputs, metal values 

are often normalized to iron or aluminum. Natural values for iron and aluminum, and many trace 

metals, also vary as a function of sediment grain size, mineralogy and organic carbon content 

with higher metal concentrations in fine-grained sediments. Without human inputs, metal concentrations are expected to co-vary with grain size and aluminum.

• Most metals were correlated with Al and grain size composition of the sediment in Kachemak 

Bay (Figure 9). Homer Harbor and station EF-4 usually had the highest concentrations.

• Mercury and selenium did not correlate with aluminum concentrations.

• Likely sources of metals in Kachemak Bay are natural bedrock weathering and material transported from mountains by rivers and streams of glacial meltwater. 
Sediment Quality Triad Assessment in Kachemak Bay 15 

40

60

80

100

120

6 7 8 9

Cr mg / kg

Al % 

Chromium

0

0.1

0.2

0.3

6 7 8 9

Cd mg / kg

Al % 

Cadmium

0.04

0.06

0.08

0.1

0.12

0.14

6 7 8 9

Hg mg / kg

Al % 

Mercury

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

6 7 8 9

Se mg / kg

Al % 

Selenium

6

8

10

12

14

16

6 7 8 9

Pb mg / kg

Al % 

Lead

30

40

50

60

6 7 8 9

Ni mg / kg

Al % 

Nickel

40

60

80

100

120

140

160

180

6 7 8 9

Zn mg / kg

Al % 

Zinc

20

30

40

50

60

70

6 7 8 9

Cu mg / kg

Al % 

Copper

Figure 9. Plots of chromium, cadmium, mercury, selenium, lead, copper, nickel and zinc (mg/kg) as 

a function of aluminum concentration in Kachemak Bay sediments. Solid triangles - Kachemak Bay; 

open squares – Homer Harbor.
16 Sediment Quality Triad Assessment in Kachemak Bay 

• Outside of the harbor, anthropogenic inputs are negligible as the human population density is 

low and no large scale industrial activities exist in the region. 

• However long range atmospheric transport is generally considered as a nonpoint source of airborn contaminants in the arctic environment (Arctic Monitoring and Assessment Program , AMAP, 

2005). Thus transboundary air pollution may contribute to the overall metals concentration in the 

region to some extent. 

4.2.4 Organic contaminants

Organic contaminants were found at low levels throughout the study area. Relative concentrations of the organic contaminants in each area are presented in Figure 10. Absolute concentrations are shown in Figure 11.

• Total PAHs concentrations in the study area were low.

• Most of organic compounds are nearly ten times higher in Homer Harbor relative to other 

areas. 

• Hexachlorocyclohexane (HCHs), which were present in subtidal and mudflat areas, were not 

detected in the Harbor. Normalized Concentration

Figure 10. Mean normalized concentrations for organic contaminants in Kachemak Bay sediments 

(site concentration of each metal and organic class was divided by the overall mean of the organic 

class).
Sediment Quality Triad Assessment in Kachemak Bay 17 

0.0

1.0

2.0

3.0

4.0

5.0

Total PCBs ng / gm

Homer Harbor

Western Subtidal Eastern Flat Eastern Subtidal

Western Flat

Port Graham

0

500

1000

1500

2000

2500

3000

Total PAH ng / gm

Homer Harbor

Eastern Flat Eastern Subtidal

Western Flat Western Subtidal

Port Graham

0.0

0.2

0.4

0.6

0.8

1.0

Total DDT ng / gm

Homer Harbor

Western Flat Western Subtidal Eastern Flat Eastern Subtidal

Port Graham

Figure 11. Concentration of Total PCBs, PAHs, and DDT in sediment from Kachemak Bay study sites.
18 Sediment Quality Triad Assessment in Kachemak Bay 

• Homer Harbor had elevated PCB concentrations (up to 4 μg/kg) while most stations were 

below 1.0 μg/kg. Elevated PCBs (2.2 ng /gm) were detected in the western intertidal area near 

Miller’s Landing. 

• Overall, PCB concentrations in the study area are very low, and even in Homer Harbor they 

are well below sediment quality guidelines.

• The distribution of total DDTs was similar to that of the PAHs. 

• Cyclodiene insecticides (chlordanes, heptachlors, nonachlors, aldrin, dieldrin, endrin and endosulfan) were also found at most sites in the study area, but concentrations were very low.

• Butyltins were above detection limits only in the harbor.

4.2.5 Comparison to other studies

Overall, the concentrations of organic contaminant including PCBs, pesticides and butyltins in 

Kachemak bay were very low. Concentration levels were comparable to the national Status and 

Trends Mussel Watch monitoring data in Alaska reported by Kimbrough et al. (2008).

4.2.6 Human versus natural sources

The levels and distributions of PAHs is of great interest in the region. In south central Alaska, the 

presence of PAHs in coastal and estuarine environments is often linked to the Exxon Valdez Oil 

Spill. Sources of PAHs are both petrogenic and pyrogenic. Petrogenic PAHs originate from natural releases from petroleum and coal deposits, or spills. Pyrogenic PAHs are formed as a result 

of combustion of organic materials such as fuel, trash, or wood. Usually, high proportions of low 

molecular weight PAHs are associated with oil and petroleum releases (petrogenic source). A 

high proportion of high weight PAHs is often linked to combustion by-products and/or long-term 

weathering. However, outside the harbor, by far the largest component of PAHs was perylene 

(Figure 12). This is a natural by-product of the breakdown of terrestrial plant material. So, the 

contribution of anthropogenic PAHs in the bay is extremely limited. Even in the harbor, the total 

concentrations are relatively low, being below the ERL guideline. 

• In Kachemak Bay the dominant PAH was perylene, usually accounting for 40-60% of the total 

PAHs. Perylene is a natural product from old plant material as opposed to petroleum, coal, or 

pyrogenic pollution sources. 

• In the harbor, total PAHs concentration varied from 1,600 to over 2,800 ng /gm. The elevated 

 concentrations of pyrene and other unsubstituted high molecular weight compounds, with lower 

concentrations of alkylated compounds, are indicative of pyrogenic sources (burned fuel).

• Aliphatic organic compound (hydrocarbons without aromatic benzene rings, e.g. PAHs) 

 characteristics did not indicate the presence of oil pollution except to a small degree within 

Homer Harbor.

• The presence of butyltins in the harbor is due to the use of antifouling paint applied to boat 

hulls. The sloughing paint chips from hulls, and the slow release from the paint into the water, 

cleaning boat hulls and uncontrolled runoff from power washing hulls that falls directly into the 

harbor increases ambient environmental levels (Figure 13).
Sediment Quality Triad Assessment in Kachemak Bay 19 

Figure 12. Top: Concentrations of individual PAHs in sediment from subtidal 

western sites. Bottom: Homer Harbor sites. Note different vertical axis scales.

• Positive correlations were recorded between sediment grain size and virtually all organic contaminants except PCBs and HCH. 

• There are no reliable records of pesticide use in the Kachemak Bay area and it is unknown if 

DDT and the other pesticides detected there were of local origin or not. The presence of these 

chemicals at concentrations above detection limits in a relatively remote and sparsely populated 

area like Kachemak Bay highlight their environmental persistence and the possible contribution 

of long range atmospheric transports (AMAP 2005). 
20 Sediment Quality Triad Assessment in Kachemak Bay 

4.3 Benthic Community Characterization

Benthic community analysis indicates the primary influences on community distributions are 

depth and proximity to the outflow from the Fox and Bradley Rivers. Stressed sites were characterized by low diversity and abundance. There were shoreline stressed sites which are exposed 

for many more hours per day than they are submerged, and many species cannot tolerate those 

conditions. There were stressed sites in the east end of the bay and one in Homer Harbor. The 

sites in the east are impacted by the high sediment loads from glacial meltwater. The Homer Harbor site was very fine grained mud which was dominated by one species. The remaining intertidal 

and subtidal habitats each contained distinct species assemblages that segregate themselves 

into turbid and clear water habitats. All sites were characterized by the presence of a small number of dominant species, and a much larger number of less numerous taxa.

Figure 13. Grids used for boat hull cleaning and maintenance operations in Homer Harbor. 

• Polychaete worms had the highest number of taxa at every station, and were the most numer

ous at all but four stations. Clams were the next most abundant taxa. Snails and crustaceans 

were more numerous and diverse in the western stations. 

• There was a strong gradient of increasing species abundance (Figure 14 Top) and diversity 

from east to west (Figure 14 Bottom). Some stations close to the shoreline also exhibited low 

abundance and diversity. 

• High diversity was negatively correlated with increasing proportions of fine grained sediment 

but positively correlated with TOC and water clarity.

• Contaminant concentrations did not appear to impact the biota. 

• The nodal analysis identified four major habitat groups shown in Figure 15. The majority of 

sites were divided into intertidal and subtidal sites, in addition to shoreline and stressed site 

clusters which were characterized by relatively low abundance and species richness (Table 4). 

• There were three main groups of species. Cosmopolitan species were found in all four types 
Sediment Quality Triad Assessment in Kachemak Bay 21 

Figure 14. Top: Benthic species abundance. Bottom: Benthic species diversity 

distribution. Strong east-west gradients of increasing species abundance and 

diversity were observed. 
22 Sediment Quality Triad Assessment in Kachemak Bay 

Table 4. Total number of taxa and abundance per square meter for stations in Kachemak Bay nodes. 

Node Station # Taxa Abundance

# m-2

Mean 

Taxa

Mean Abundance

Subtidal

ES1 58 14,025

ES2 46 8,450

ES5 48 18,625

ES7 48 11,875

HH1 59 15,225

HH2 43 10,825

WF2 61 19,225 56.8 14,267.3

WS1 62 12,625

WS2 78 14,475

WS3 59 11,225

WS3X 58 17,275

WS4 61 14,350

WS5 58 17,275

Intertidal

EF1 32 10,175

EF2 22 17,200

EF3 33 12,350

EF5 52 13,425

WF1 51 8,500 39.1 11,681.3

WF3 39 10,475

WF4 50 13,475

WF5 34 7,850

Tidal Stress

EF6 10 7,000

EF7 16 9,175 15.3 6,558.3

WF6 20 3,500

Glacial Stress

EF4 11 650

ES3 11 2,000

ES4 18 8,150 14.4 5,200.0

ES6 17 850

HH3 15 14,350

of sites. Subtidal species were found mostly below tide and intertidal species were found

above the low tide line. 

• This study did not assess deeper areas of Kachemak Bay. Beyond the 10 fathom isobath the bottom drops off to a deeper basin. Samples taken in 2008 revealed a more diverse community than 

that found on the shelf. Monitoring in Port Valdez reveals a very similar species distribution on 

shelf stations and greater diversity at depth (Blanchard et al. 2002). 
Sediment Quality Triad Assessment in Kachemak Bay 23 

Figure 15. Benthic species nodal distribution.

4.4 Sediment Toxicity 

In general, no significant toxicity was observed in any of the areas including Homer Harbor. 

• The Eohaustorius estuarius, bioassay demonstrated significant toxicity at one station near the 

Fox River (Figure 16 Top). The site had extremely fine grained muddy sediment but also had 

elevated metals concentrations.

• The Ampelisca abdita bioassays demonstrated significantly reduced survival at only one station 

in Coal Bay Figure 16 Bottom. While survival was statistically reduced relative to controls, it was 

above 80% and is therefore considered to be an indicator of only marginal effect. 

5.0 Supplemental Samples at Port Graham

While the concentration distributions are instructive relative to fate and transport processes, none 

of the levels at any location indicate the potential for immediate concern. PCBs and mercury 

do bioaccumulate in the food chain however, so source identification and reduction should be a 

management objective. 

5.1 Organics and metals concentrations

• One station in Port Graham had a similar distribution of PAHs as was found in Homer Harbor 

(Figure 11), with indications of contributions from fuel and combustion by-products (Figure 17). 
24 Sediment Quality Triad Assessment in Kachemak Bay 

Figure 16. Top: Eohaustorius estuarius, bioassays demonstrated significant toxicity at one 

station near the Fox River. Bottom: Ampelisca abdita bioassay demonstrated significantly 

reduced survival at one station in Coal Bay.
Sediment Quality Triad Assessment in Kachemak Bay 25 

0

25

50

75

100

125

PAH ng / gm

PG-2 PG-3C PG-4b

Figure 17 . Concentrations of individual PAH compounds found at three Port Graham stations. The 

PAH signature for Port Graham appears slightly different from other Kachemak Bay study sites, indicative of source differences. Site PG3c resembles Homer Harbor.

• The single station in Port Graham where PAHs were elevated, also had elevated PCBs relative to 

the other stations, but was below the levels in Homer Harbor (Figure 11). 

• Concentrations of DDT showed a slightly different pattern, in which the highest concentration was 

seen at Port Graham (Figure 11).

• The remaining pesticides and related compounds were generally found at or below detection 

limits.

• Metals concentrations in greater Kachemak Bay and Port Graham Bay sediments were quite 

different and may be an indication of significant differences in geologic composition of the watershed as much as man-made contamination. 

• Cadmium, mercury, and selenium were elevated 4-6 times above the average levels at station 

PG-3c (Figure 18A). Chromium, selenium, and cadmium were elevated at station PG-4b, located 

toward the head of the bay. Conversely, arsenic, antimony, and lead at all three Port Graham 
26 Sediment Quality Triad Assessment in Kachemak Bay 

0

100

200

300

400

500

600

700

Percent of Mean Concentration

Cd Cr Hg Se

Figure 18A. Relative concentrations of four elements (cadmium, chromium, mercury, selenium) in 

Kachemak Bay sampling areas and extra sampling stations at Port Graham. Concentrations are 

normalized to the overall mean concentration in the Kachemak Bay only (excluding Port Graham) and 

expressed as a percentage.

sites were approximately half the concentrations seen in Kacheamk Bay (Figure 18B). Concentrations at station PG-2, located directly across the bay from the village were otherwise unremarkable. 

• Given the well documented harmful biological consequences of cadmium, mercury, chromium 

and selenium, a follow-up study to assess bioavailability and bioaccumulation may be warranted.

5.2 Benthos and sediment toxicity

• Sediment toxicity tests at Port Graham showed significant toxicity results only with A. abdita at 

station PG3c. Survival was reduced to 68.8%. All the other tests resulted in survival rates of 90% 

or more. Significant reduction in survival was not observed in the E. estuarius bioassays. 

• Samples were also taken at Port Graham to assess the presence of Clostridium perfringens 

in the sediment as an indicator of possible sewage contamination. C. perfringens counts were 
Sediment Quality Triad Assessment in Kachemak Bay 27 

0

50

100

150

200

250

Percent of Mean Concentration

As Pb Sb

Figure 18B. Relative concentrations of three elements (arsenic, lead, antimony) in Kachemak Bay 

sampling areas and extra sampling stations at Port Graham. Concentrations are normalized to the 

overall mean concentration in the Kachemak Bay only (excluding Port Graham) and expressed as a 

percentage.

elevated at station PG3c relative to the other stations (436/gm wet vs. 85 and 161). Sediment 

quality guidelines for C. perfringens do not currently exist. While the value at station PG3c is well 

below what might be expected in the proximity of a sewage outfall, it is elevated relative to the 

other stations, indicating that conditions favor propagation of pathogenic bacteria. The sediments 

were organically enriched and anoxic. In the NS&T data base, values of 500 or more spores /gm 

are generally (but not always) found in the vicinity of urban areas.

• Of the 239 total taxa found in Kachemak Bay, 79 were also found in Port Graham. However, 45 

taxa were identified in Port Graham that were not seen in the larger bay. None of the Port Graham stations were intertidal, so that portion of the community was largely missing. In addition, the 

species in deep sandy habitats found in the larger bay were absent in Port Graham. Port Graham 

station PG3c was particularly depauperate in diversity.
28 Sediment Quality Triad Assessment in Kachemak Bay 

6. CONCLUSION

A better comparison of data sets is a contrast with other Bioeffects Project’s sediment data. The mean 

ERM quotient is the average of the ratio of ERM values to sediment concentrations for each chemical. Calculating the ERM quotient for all chemicals from a variety of locations and plotting them on 

a scale of 1-100 reveals the relative contamination levels of the locations. Figure 19 shows the relative position of Kachemak Bay, Port Graham, and Homer Harbor in relation to several other systems 

(Hartwell et al. 2001; Hartwell and Hameedi, 2007; Hartwell et al. 2007; Lauenstein and Kimbrough 

2007; Long et al. 1995). ERM quotients for Delaware, Chesapeake, and Massachusetts Bays are 

derived from open water sites away from harbors and tributaries, and are thus comparable to Kachemak Bay and Port Graham sites. The harbor sites ERM quotients are derived from sampling in areas 

specifically within commercial harbor areas and are thus comparable to Homer Harbor. While the 

Homer Harbor ERM quotient is far below the other harbors, those harbors are in large metropolitan 

areas with heavy industry and commercial shipping facilities.

ACKNOWLEDGEMENTS

We gratefully acknowledge the North Pacific Research Board for major funding support. The Cook 

Inlet Regional Citizens Advisory Council also provided funding to support field work. The Kachemak 

Bay National Estuarine Research Reserve and Kasitsna Bay Lab provided logistical support. Capt. 

John Crosbie and Everett Anderson worked tirelessly aboard the vessel Columbia. Mark Janes and 

Tim Robertson of Nuka Research also assisted in the field work. Allan Fukuyama of Fukuyama-Hironaka Taxonomic & Environmental Inc., Dan Johnson of TRAC Laboratories Inc., and Juan Ramirez of 

TDI Brooks International conducted the laboratory analyses. 

Figure 19. Distribution of ERM quotients in Kachemak Bay, Port Graham, and Homer Harbor relative 

to open water reaches of other bays, and large ports around the United States.
Sediment Quality Triad Assessment in Kachemak Bay 29 

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Sediment Quality Triad Assessment in Kachemak Bay: 

Characterization of Soft Bottom Benthic Habitats and 

Contaminant Bioeffects Assessment

S. Ian Hartwell, A. Dennis Apeti, W. Larry Claflin, W. Edward Johnson, 

and L. Kimani Kimbrough

National Oceanic and Atmospheric Administration