NOAA Technical Memorandum NMFS-AFSC-139


A Survey of Fish Assemblages 

in Eelgrass and Kelp Habitats 

of Southeastern Alaska 

by 

S. W. Johnson, M. L. Murphy, D. J. Csepp,

P. M. Harris, and J. F. Thedinga

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration 

National Marine Fisheries Service 

Alaska Fisheries Science Center 

September 2003 
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NOAA Technical Memorandum NMFS-AFSC-139


A Survey of Fish Assemblages 

in Eelgrass and Kelp Habitats 

of Southeastern Alaska 

by 

S. W. Johnson, M. L. Murphy, D. J. Csepp,

P. M. Harris, and J. F. Thedinga

Alaska Fisheries Science Center 

7600 Sand Point Way N.E. 

Seattle, WA 98115 

www.afsc.noaa.gov 

U.S. DEPARTMENT OF COMMERCE

Donald L. Evans, Secretary 

National Oceanic and Atmospheric Administration 

Vice Admiral Conrad C. Lautenbacher, Jr., U.S. Navy (ret.), Under Secretary and Administrator 

National Marine Fisheries Service 

William T. Hogarth, Assistant Administrator for Fisheries 

September 2003 
This document is available to the public through: 

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U.S. Department of Commerce

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Springfield, VA 22161 

www.ntis.gov 
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iii 

ABSTRACT 

For most federally managed fish species in Alaska, basic information on distribution and 

use of nearshore marine habitats is lacking, especially for early life stages. To gain a better 

understanding on the use and importance of nearshore habitats as essential fish habitat (EFH), we 

compared fish assemblages between two distinct habitat types (eelgrass, Zostera marina, and 

kelp, mostly Laminaria saccharina) at 30 sites in southeastern Alaska from 1998 to 2000. Sites 

were selected in four regions to cover a geographical gradient from north to south and from 

inside to outside waters. Fish were collected by beach seine from June through August each 

year. A total of 102 seine hauls yielded more than 51,000 fish comprising 54 species; 23 of the 

species that we captured are included in a salmon or groundfish fishery management plan in 

Alaska. 

Species richness was greater in eelgrass than in kelp, whereas the Shannon-Wiener 

diversity index (HN) was similar between habitat types. Abundance of fish varied considerably 

between habitat types and among regions, often because of the patchy distribution of some 

species. Distribution patterns were evident for some species by differences in catch among 

regions. 

 Eelgrass and kelp support high biodiversity and are important habitats for juveniles of 

many commercially important or forage fish species. Knowledge of fish assemblages and their 

use of intertidal and shallow, subtidal vegetation will help managers identify EFH. Once 
iv 

identified, managers can then make recommendations to protect or minimize impacts to EFH 

from human disturbance. 
v 

CONTENTS 

Abstract .................................................................... iii


Introduction .................................................................. 1


Materials and Methods .......................................................... 2


Data Analysis ................................................................. 5


Results ...................................................................... 6


Discussion .................................................................. 10


Acknowledgments ............................................................ 16


Citations .................................................................... 18


Tables ...................................................................... 25 


Figures ..................................................................... 33 

INTRODUCTION 

One of the most important changes in the 1996 reauthorization of the Magnuson-Stevens 

Fishery Conservation and Management Act was a requirement to identify and describe essential 

fish habitat (EFH) for species included in federal fishery management plans (FMPs) (National 

Marine Fisheries Service 1999). The amended act gave heightened importance to fish habitat in 

resource management decisions. Essential fish habitat is defined as those waters and substrate 

necessary for spawning, breeding, feeding, or growth to maturity (North Pacific Fishery 

Management Council 1998). Identifying EFH requires basic information on fish distribution and 

habitat use. Such information is lacking, however, for many FMP species in Alaska, especially 

for early life stages. 

Within federally mandated EFH habitat designations in Alaska, nearshore areas of intertidal 

and subtidal vegetation are considered habitat areas of particular concern because of their high 

value as fish habitat and their vulnerability to human disturbance (North Pacific Fishery 

Management Council 2002). Alaska has about 55,000 km of shoreline-- nearly two-thirds the 

coastline length of the conterminous 48 states (Heard and Andersen 1999)--and a wide diversity 

of vegetated estuarine and marine habitats (Glass 1996). Two types of submerged vegetation, 

eelgrass (Zostera marina) and kelps (e.g., Laminaria saccharina), are widely distributed in lower 

intertidal and shallow subtidal areas along the Pacific coast of the United States, including 

Alaska (McRoy 1968, Phillips and Watson 1984, Fonseca et al. 1998, O’Clair and Lindstrom 

2000). Only about 35% of Alaska, however, has been mapped to determine the acreage of these 

vegetated habitat types (National Wetland Inventory staff, U.S. Fish and Wildlife Service, 1011 
2


E. Tudor Rd., Anchorage, AK 99503. Pers. commun., October 2000) and few studies have 

examined eelgrass and kelp as fish habitat. 

Submerged vegetation provides food resources, cover, and nursery habitat for many marine 

species important in sport and commercial fisheries (Thayer et al. 1978, Gotceitas et al. 1997, 

Valle et al. 1999, Dean et al. 2000). Worldwide, species from more than 50 families of fish have 

been found in seagrass habitats (Pollard 1984). Of the few studies done in Alaska, important 

commercial species found in eelgrass or kelp have included Pacific herring (Clupea pallasi), 

juvenile Pacific cod (Gadus macrocephalus), juvenile rockfish (Sebastes spp.), and juvenile 

salmon (Oncorhynchus spp.) (Laur and Haldorson 1996, Dean et al. 2000, Murphy et al. 2000, 

Byerly 2001). 

To gather fish distribution and habitat use information necessary to identify EFH, we 

conducted a survey of eelgrass and kelp habitats throughout southeastern Alaska. Our objectives 

were to 1) identify and compare fish assemblages in each habitat type and 2) examine patterns in 

the distribution of fish within each habitat type among northern and southern, inside and outside 

waters. This report focuses on the most abundant species found in each habitat type and those 

species included in an FMP for Alaska (North Pacific Fishery Management Council 1998, 2002). 

Because nearshore, vegetated habitats have a high potential to be affected by shoreline 

development, the role of these habitats as rearing or spawning areas for commercially important 

species needs to be documented to identify and conserve EFH. 
3 

MATERIALS AND METHODS 

Fish assemblages were sampled at 30 sites throughout southeastern Alaska from 1998 to 

2000 (Fig. 1). Sampling was conducted from June to August each year. Sites were selected in 

four regions to cover a geographical gradient from north to south and from inside to outside 

waters. Marine waters of southeastern Alaska are characterized by an inshore-offshore salinity 

gradient (Murphy and Orsi 1999) and a north-south temperature gradient (Quast 1968). We chose 

Frederick Sound as the division between northern and southern regions, similar to the boundary 

chosen by Quast (1968) (Fig. 1). Sites on or near the outer coast or near major ocean entrances 

were considered outside waters, whereas all other sites were considered inside waters (Fig. 1). 

Initially, we attempted to sample eelgrass and kelp at all sites, but this was not possible because 

eelgrass or kelp habitats were absent or of minimal size at some sites. Thus, at 10 sites only 

eelgrass was sampled, at 5 sites only kelp, and at 15 sites both eelgrass and kelp were sampled 

(Fig. 1). Five sites were sampled in 1998, 11 sites in 1999, and 14 sites in 2000. 

Most eelgrass sites were located inside protected bays and inlets with freshwater influence, 

whereas most kelp sites were more oceanic and located in exposed locations at the mouths of 

bays. Relative to mean lower low water (MLLW), eelgrass occupies areas of the lower intertidal 

and subtidal zones from +1 m to !6 m, and understory kelp occupies subtidal areas to depths of 

about !30 m. Eelgrass usually grows in soft substrates of sand or mud. Understory kelp often 

grows as dense, low-lying mats on rocky substrates. Kelp habitats that we sampled were 

dominated by L. saccharina. This is a brown kelp that has a smooth blade up to 3.5 m long and 
4


18 cm wide (O’Clair and Lindstrom 2000). Other kelps commonly found with L. saccharina 

were Cymathere triplicata and two or more species of Alaria. 

Fish were sampled with a 37-m long variable-mesh beach seine that tapered from 5 m wide at 

the center to 1 m wide at the ends. Outer panels were each 10 m of 32-mm stretch mesh, 

intermediate panels were each 4 m of 6-mm square mesh, and the bunt was 9 m of 3.2-mm square 

mesh. We set the seine as a “round haul” by holding one end on the beach, backing around in a 

skiff with the other end to the beach about 18 m from the start, and pulling the seine onto shore. 

The seine had a lead line and a float line so that the bottom contacted the substrate and the top 

floated. A more complete description of the beach seine and our methods of setting it are 

provided in Murphy et al. (2000). 

Two beach seine hauls were usually made in each habitat type at each site. Exceptions were 

one seine haul at Auke Bay (Site 3) and from four to six hauls each at Yakobi Island (Site 6), 

Sitka (Site 18), Heceta Island (Site 26), and Craig (Site 27) (Fig. 1). Seine hauls were at least 

50 m apart. All sampling occurred within 2 hours of low tide (range +1.0 to !1.5 m below 

MLLW). 

Captured fish were identified to species and enumerated. Number of fish in large catches 

was visually estimated for some species (e.g., Pacific herring). Fork length (FL) was measured to 

the nearest millimeter for up to 50 individuals of selected species including gadids, Pacific 

herring, Pacific sand lance (Ammodytes hexapterus), and rockfish. Fish were anesthetized with 

MS-222 for identification and measurement. Fish that could not be identified in the field were 

frozen and later identified in the laboratory. 
5


At most seine haul sites, we measured selected eelgrass and kelp characteristics and recorded 

temperature and salinity. At eelgrass sites, a transect was laid parallel to shore approximately 

0.5 m below MLLW, and three 313-cm2

 quadrats were placed about 5 m apart on the transect. 

Eelgrass shoots within each quadrat were cut at the substrate surface and rinsed to remove 

sediments and detritus. Loose epiphytic algae was removed manually. We counted all eelgrass 

shoots in each sample and placed them in plastic bags. In the laboratory, samples were dried at 

60°C to a constant weight and were weighed to the nearest 0.1 g. Similarly, at kelp sites, all kelp 

within three 0.5-m2

 quadrats was collected, identified, and weighed. Kelp was placed in a mesh 

bag and spun by hand for about 30 seconds to remove excess water and was then weighed to the 

nearest 0.1 kg. Temperature and salinity at 30-cm depth were measured with a thermometer and 

refractometer, respectively. 

DATA ANALYSIS

 This study was designed to provide a descriptive analysis of species presence or absence in 

two distinct habitat types. All catch data was standardized to catch per seine haul by dividing the 

total catch of each species by the number of seine hauls in each habitat type at each site. To show 

the wide distribution of catch data, we used box-and-whisker plots (Figs. 2 to 5). The bottom of 

the box represents the first quartile, the top of the box the third quartile, and a line drawn across 

the box represents the median. Whiskers extend from the top and bottom of the box to (usually) 

the lowest and highest observations; outliers are shown as solid circles (MINITAB 2000). Catch 

data was characterized by small numbers or zeros for many species, often resulting in a median 
6 

catch of zero. Species richness refers to the total number of species found in a given habitat type 

or location. Species diversity was calculated by the Shannon-Wiener diversity index (HN) 

described in the following equation 

s 

HN = − =1 

∑

i 

pi ln pi , 

where s is the number of species, and pi is the proportion of the total number of individuals 

consisting of the i

th species (Poole 1974). Two components of diversity are combined in this 

index: 1) number of species and 2) evenness in number of individuals among species. 

RESULTS 

A total of 102 seine hauls yielded more than 51,000 fish comprising 54 species, including 23 

FMP species (Table 1). Total catch for all years was dominated by Pacific herring and shiner 

perch (Cymatogaster aggregata) that were sometimes captured in large numbers. Based on 

percent of total catch, the 10 most abundant species were Pacific herring (50.9%), shiner perch 

(18.3%), crescent gunnels (Pholis laeta; 4.9%), juvenile chum salmon (O. keta; 4.7%), Pacific 

sand lance (3.4%), threespine stickleback (Gasterosteus aculeatus; 3.2%), bay pipefish 

(Syngnathus leptorhynchus; 2.6%), snake prickleback (Lumpenus sagitta; 1.7%), tube-snout 

(Aulorhynchus flavidus; 1.3%), and juvenile pink salmon (O. gorbuscha; 1.1%). In addition to 

Pacific herring and salmon, other species captured that are important in sport or commercial 

fisheries were cutthroat trout (O. clarki), Dolly Varden (Salvelinus malma), lingcod (Ophiodon 
7


elongatus), Pacific cod, rockfish (six species), and walleye pollock (Theragra chalcogramma). 

Capture locations for all FMP species are identified in Table 2. 

Species richness varied by habitat type and region. For example, number of species ranged 

from 5 to 22 among eelgrass sites and from 7 to 20 among kelp sites (Table 3). Inclusive of all 

sites, number of species was greater in eelgrass (median = 14) than in kelp (median = 11). By 

region, median number of species in eelgrass ranged from 12 in northern outside waters to 20 in 

southern outside waters. Similarly, median number of species in kelp ranged from 9 in southern 

inside waters to 11 in northern inside and southern outside waters (Table 3). 

Species diversity was similar between habitat types, but varied among regions, particularly 

among kelp sites (Table 3). Inclusive of all sites, the median Shannon-Wiener diversity index 

(HN) was 1.52 in eelgrass (range 0.04!2.32) and 1.43 in kelp (range 0.06!2.23). Among eelgrass 

sites, (HN) was lowest in southern inside waters (median = 1.34) and greatest in southern outside 

waters (median = 1.74) (Table 3). Among kelp sites, (HN) was lowest in northern outside waters 

(median = 0.12) and greatest in southern outside waters (median = 1.98) (Table 3). High 

abundance of Pacific herring at two kelp sites (Port Althorp-Site 5 and Yakobi Island-Site 6) 

greatly reduced diversity in northern outside waters (Table 3; Fig. 1). 

Catch per seine haul (all species) varied considerably between habitat types and among 

regions within habitat types (Fig. 2), often because of the patchy distribution of some species. 

Inclusive of all sites, median catch per haul was greater in eelgrass (199 fish) than in kelp (82 

fish); catches ranged from a low of about 10 to more than 2,500 fish in both habitat types (Fig. 2). 

Large catches were often dominated by single species such as Pacific herring or shiner perch. By 

region, median catch per haul in eelgrass ranged from 159 fish in northern outside waters to 320 
8


fish in southern outside waters. Similarly, median catch per haul in kelp ranged from 30 fish in 

northern inside waters to 2,528 fish in northern outside waters (Fig. 2). 

Abundance of Pacific herring and sand lance, important forage species, was extremely 

variable with most fish only caught in a few seine hauls. For example, catch per haul of these 

species was greater than or equal to 2,500 fish at four sites (Bridget Cove-Site 1, Port Althorp-Site 

5, Port Camden-Site 19, and Yakobi Island-Site 6; Fig. 1) and zero fish at 15 sites. Infrequent 

catches of forage fish in both habitat types resulted in a median catch per haul of less than or equal 

to 0.1 fish in most regions (Fig. 3). Of the more than 26,000 herring captured, 77% were in kelp, 

whereas of the more than 1,700 sand lance captured, 60% were in eelgrass (Table 1). All herring 

and most sand lance captured were juveniles. Mean FL was 55 mm (range 27!115 mm; n = 178) 

for Pacific herring and 82 mm (range 52!122 mm; n = 120) for sand lance. 

Most chum, pink, and coho salmon were captured at one site that was sampled in June. Of 

the total 2,447 chum and 562 pink salmon captured, 62% and 95%, respectively, were captured in 

kelp at Kelp Bay (Site 14, Fig. 1). All chum and pink salmon were juveniles; mean FL was 

58 mm (range 37!88 mm; n = 196) for chum salmon and 42 mm (range 30!64 mm; n = 52) for 

pink salmon. Of the 333 coho salmon captured, 73% were in eelgrass at Cosmos Cove (just south 

of Kelp Bay). Most coho salmon captured were smolts; mean size was 119 mm (range 90-135 

mm; n = 26). 

 Of the 759 gadids captured, 57% were walleye pollock and 43% Pacific cod. Catch of 

gadids was similar in eelgrass and kelp (Table 1). Similar to Pacific herring and sand lance, catch 

of gadids was also extremely variable with most fish caught at only a few sites. Numerous low or 

zero catches of gadids (all species) in both habitat types, resulted in a median catch per haul of 
9


less than or equal to 1 in all regions (Fig. 4). All gadids captured were juveniles. Mean FL was 

67 mm (range 25!148 mm; n = 189) for walleye pollock and 71 mm (range 35!190 mm; n = 156) 

for Pacific cod. 

Of the 477 rockfish captured, most were copper (S. caurinus; 60%) and black (S. melanops; 

25%) rockfish. Other species captured included brown (S. auriculatus), dusky (S. ciliatus), 

quillback (S. maliger), and yellowtail (S. flavidus) rockfish. For most rockfish species, total catch 

was greater in eelgrass than in kelp (Table 1). In each habitat type, median catch per haul of 

rockfish was greater in northern and southern outside waters (range 4.8-9.5 fish) than in northern 

and southern inside waters; few rockfish were captured in inside waters (Fig. 5). Most rockfish 

captured were juveniles; mean FL (all species) was 107 mm (range 49!231 mm; n = 475). 

Other abundant species included bay pipefish, crescent gunnel, shiner perch, snake 

prickleback, threespine stickleback, and tube-snout. Total catch of these species was greater in 

eelgrass than in kelp; few bay pipefish, snake prickleback, threespine stickleback, and tubesnout 

were captured in kelp (Table 1). Catch of these species varied by region within each habitat type. 

For example, among eelgrass sites, median catch per haul of shiner perch was greater in northern 

and southern outside waters (64 and 18 fish, respectively) than in comparable inside waters 

(<5 fish); no shiner perch were captured in northern inside waters. 

Some of the less abundant FMP species captured in eelgrass and kelp included flatfish, Arctic 

shanny (Stichaeus punctatus), Pacific sandfish (Trichodon trichodon), penpoint gunnel 

(Apodichthys flavidus), red Irish lord (Hemilepidotus hemilepidotus), and surf smelt (Hypomesus 

pretiosus) (Table 1). Only 68 flatfish were caught consisting of 6 species: 31 rock sole 

(Lepidopsetta bilineata), 17 Pacific sanddab (Citharichthys sordidus), 11 yellowfin sole (Limanda 
10


asper), 4 starry flounder (Platichthys stellatus), 3 English sole (Parophrys vetulus), and 2 butter 

sole (Isopsetta isolepis). All were juveniles and most (59%) were captured in eelgrass. Mean FL 

of flatfish was 112 mm (range 92!150 mm; n = 7). For the rest of the species mentioned above, 

numbers captured were small (<180 fish) and most were in eelgrass (Table 1; Table 2). 

Based on frequency of occurrence at all sites sampled, the two most ubiquitous species were 

crescent gunnels and northern sculpin (Icelinus borealis). Crescent gunnels were captured at all 

eelgrass and kelp sites, whereas northern sculpin were captured at 92% of the eelgrass sites and 

94% of the kelp sites (Fig. 6). Species not already mentioned and found in at least 50% of all 

eelgrass or kelp sites were Pacific staghorn sculpin (Leptocottus armatus), buffalo sculpin 

(Enophrys bison), great sculpin (Myoxocephalus polyacanthocephalus), and silverspotted sculpin 

(Blepsias cirrhosus). 

Eelgrass shoot density and biomass and kelp biomass were similar among regions (Fig. 7). 

Mean density ranged from 624 shoots/m2

 in northern inside waters to 985 shoots/m2 in southern 

inside waters. Eelgrass biomass (dry weight) ranged from a mean of 62.3 g/m2 in southern inside 

waters to 129.9 g/m2

 in southern outside waters. Kelp biomass (wet weight) was similar in all 

regions and averaged about 3.5 kg/m2. 

At the 15 sites where both habitat types were sampled, water temperatures were often higher 

(7 of 15 sites) and salinities lower (10 of 15 sites) in eelgrass than in kelp. Among eelgrass sites 

by region, mean water temperature ranged from 12.3°C in southern inside waters to 14.0°C in 

northern outside waters, and mean salinity ranged from 19.7 PSS in northern inside waters to 

28.7 PSS in southern outside waters. Similarly, among kelp sites, mean water temperature ranged 
11


from 11.8°C in southern inside waters to 12.4°C in southern outside waters, and mean salinity 

ranged from 26.8 PSS in southern inside waters to 31.8 PSS in southern outside waters. 

DISCUSSION 

Submerged vegetation provides habitat structure and complexity and attracts diverse 

assemblages of fish. More than 50 species of marine fish, many of commercial importance, use 

eelgrass and kelp habitats in southeastern Alaska. Commercially important species that we 

captured, mostly as juveniles, included flatfish, Pacific cod, Pacific herring, rockfish, salmon, and 

walleye pollock. Most of these are target species in either a groundfish or salmon FMP in Alaska 

(North Pacific Fishery Management Council 1998, 2002). The presence of juveniles in eelgrass 

and kelp indicate that these habitats may be important nursery areas for some species. Abundant 

non-commercial species were shiner perch, crescent gunnel, threespine stickleback, and bay 

pipefish. Gunnels are included in the forage fish category in the FMP for groundfish in the Gulf 

of Alaska (North Pacific Fishery Management Council 2002). Similar fish assemblages in 

eelgrass and kelp have been observed in other areas of Alaska and the northeast Pacific Ocean 

(Phillips and Watson 1984, Laur and Haldorson 1996, Dean et al. 2000, Murphy et al. 2000). 

Species richness was higher in eelgrass than in kelp, whereas species diversity was similar 

between habitat types. Near Craig, Alaska, Murphy et al. (2000) found no difference in species 

richness and diversity between eelgrass and kelp, but did catch significantly more fish in eelgrass. 

Although our catch data varied considerably between habitat types, median catch per haul (all 

species) was more than twice as great in eelgrass (199 fish) than in kelp (82 fish). Regardless of 
12


plant type, submerged vegetation offers increased habitat complexity (via plant density and 

morphology) otherwise lacking on bare or sparsely covered bottoms (Heck and Orth 1980). 

Higher species richness, diversity, and abundance of fish in vegetated versus unvegetated bottoms 

has been reported in many areas (Briggs and O’Connor 1971, Orth and Heck 1980, Orth et al. 

1984, Lubbers et al. 1990, Sogard and Able 1991, Connolly 1994, Lazzari and Tupper 2002, 

Wyda et al. 2002). 

Herring and sand lance may utilize eelgrass and kelp differently. Both of these species 

school, which may explain the highly variable and sometimes large catches at some sites. Herring 

are important in commercial and subsistence fisheries in Alaska, and along with sand lance, are 

key forage fish for other species of fish, birds, and marine mammals (Dick and Warner 1982, Paul 

and Paul 1998). Sand lance are included in the forage fish category in the FMP for groundfish in 

the Gulf of Alaska (North Pacific Fishery Management Council 2002), whereas herring are 

managed by the state of Alaska and are not an FMP species. The temporal extent to which herring 

and sand lance use eelgrass or kelp is unknown; we sampled only in summer. Because sand lance 

spawn on beaches of sand and gravel in fall (Dick and Warner 1982), use of eelgrass and kelp is 

probably limited to summer rearing of juveniles. Herring, however, use submerged vegetation for 

rearing and as a spawning substrate in spring (Phillips and Watson 1984). In Boca de Quadra, 

southeastern Alaska, eelgrass and kelp are the dominant vegetation types used as spawning 

substrates (Blankenbeckler and Larson 1982), whereas in Washington, eelgrass is the dominant 

vegetation type that receives herring spawn (Stick 1995). 

At one of the few sites that we sampled in June, the catch was dominated by juvenile salmon 

and most were caught in kelp. Few salmon were captured at sites sampled in July and August. 
13


Pink and chum salmon fry are abundant in nearshore waters of Alaska from mid-April to midJune (Jaenicke et al. 1984, Celewycz et al. 1994), often in schools of thousands of fish (Heard 

1991). Whether salmon fry only transit through eelgrass and kelp on their way from estuaries to 

offshore waters or use submerged vegetation as nursery areas is unclear. Nearshore habitats can 

provide food and cover for salmon fry, or protection from wind-generated waves and strong tidal 

currents (Celewycz et al. 1994). Murphy et al. (2000), however, found no difference in catch of 

juvenile pink and chum salmon between vegetated and sparsely vegetated sites near Craig, 

Alaska. 

Juvenile Pacific cod and walleye pollock were captured in eelgrass and kelp but were not 

very abundant. Murphy et al. (2000) also found few Pacific cod or pollock in eelgrass or kelp. In 

Prince William Sound, Alaska, however, juvenile Pacific cod are abundant in eelgrass (Laur and 

Haldorson 1996, Dean et al. 2000). Similarly, in Nova Scotia, juvenile Atlantic cod (Gadus 

morhua) use eelgrass (Tupper and Boutilier 1995), possibly as refuge habitat from predators 

(Gotceitas et al. 1997). We cannot explain the lack of association between Pacific cod and 

eelgrass in southeastern Alaska. In another study, we captured with beach seines and observed 

with an ROV (remotely operated vehicle) hundreds of thousands of juvenile gadids (mostly 

pollock) in kelp near the Brothers Islands, southeastern Alaska1

, possibly indicating that gadids 

may have spatially discrete nursery areas. 

Several species of rockfish recruit as pelagic larvae to some type of substrate including 

submerged vegetation (Love et al. 1991, Murphy et al. 2000, Byerly 2001). We found juveniles of 

1

 S. W. Johnson, unpubl. data. Auke Bay Laboratory, Alaska Fish. Sci. Cent., 11305 

Glacier Hwy., Juneau, AK 99801-8626. 
14


six species of rockfish in eelgrass and kelp; copper and black rockfish were the two most 

abundant species. Three of the species that we captured (copper, dusky, and quillback rockfish) 

are included in the FMP for groundfish in the Gulf of Alaska (North Pacific Fishery Management 

Council 2002). Juvenile rockfish may use shallow, submerged vegetation for summer rearing 

only. In Puget Sound, Washington, brown, copper, and quillback rockfish occupy eelgrass and 

low-relief rocky areas with kelp in summer but are mostly absent in winter (Matthews 1990). In 

Yaquina Bay, Oregon, Bayer (1981) captured juvenile black rockfish in eelgrass from March 

through October. In a mark-recapture study near Sitka, Alaska, juvenile copper rockfish were 

found in the same eelgrass or kelp bed from May to August (Byerly 2001). Year-round sampling 

is needed to determine the seasonal utilization of vegetated habitats by juvenile rockfish in 

southeastern Alaska. Juvenile rockfish may migrate from shallow, nearshore habitats in summer 

to deeper water in winter (Moulton 1977). In Washington and British Columbia, copper rockfish 

hide in crevices of rocky substrates and become inactive in fall and winter (Patten 1973, Richards 

1987). 

Differences in water temperature, salinity, cover, food, and presence of predators likely 

accounts for some of the different distribution and abundance patterns that we observed among 

study sites. In Kachemak Bay, Alaska, differences in the distribution and abundance of nearshore 

fish between inner and outer bay sites corresponded to differences in temperature and salinity 

(Abookire et al. 2000). Many eelgrass sites that we sampled were inside sheltered bays with 

warmer, less saline surface waters than more exposed areas with kelp. Warmer water can enhance 

growth and survival of juvenile fish (Gadomski and Caddell 1991, Gibson 1994) and the input of 

stream nutrients can increase food production (St. John et al. 1992). This may partially explain 
15


why gunnels, pipefish, pricklebacks, sticklebacks, and tube-snouts were more abundant in eelgrass 

than in kelp. In addition, these species may be particularly well-adapted to eelgrass because they 

feed on small crustaceans (Hart 1973) that, in turn, depend on eelgrass detritus (Pollard 1984). 

Distribution may also be influenced by species seeking eelgrass or kelp to escape predators 

(Gotceitas et al. 1995). Greenlings (Hexagrammidae) and cottids, however, were common in both 

habitat types and are predators of juvenile salmon and gadids (Hart 1973, Celewycz et al. 1994). 

Thus, a trade-off exists between using vegetated habitats for food resources and increased risk to 

predation. 

Proximity to spawning areas may also affect the geographical distribution and abundance of 

some species. For example, we captured most juvenile rockfish at sites on or near the outer coast; 

few rockfish were captured in inside waters. The two most abundant species that we captured in 

eelgrass or kelp were black and copper rockfish. Adult black rockfish are more abundant in 

outside coastal waters than in inside waters, often in large schools (Rosenthal et al. 1982, Humann 

1996) and no adult copper rockfish were observed in an ROV survey of northern inside waters (S. 

W. Johnson, unpubl. data). Thus, larvae spawned from adults of these species are more likely to 

“settle and stay” in vegetated habitats near the outer coast than in inside waters. Reasons for the 

complete absence of rockfish at some inside sites (e.g., Auke Bay-Site 3, Bridget Cove-Site 1, 

Funter Bay-Site 4, St. James Bay-Site 2; Fig. 1), however, are unclear. Juvenile dusky, quillback, 

and yellowtail rockfish use submerged vegetation and adults of these species are present in 

northern inside waters (Carlson and Barr 1977, Carlson 1986, S. W. Johnson, unpubl. data). 

Assuming that these rockfish spawn in inside waters, we would expect some juveniles to rear in 

eelgrass or kelp. Natural variability among individual sites in temperature, salinity, or vegetation 
16


characteristics, however, may limit or exclude rockfish recruitment. Additionally, larval mortality 

may be higher in inside waters than outside waters or juveniles may utilize other habitats in inside 

waters that we did not sample. 

Regional differences in distribution and abundance were expected for some species. For 

example, shiner perch were not captured in northern inside waters in eelgrass or kelp. This was 

expected because shiner perch prefer more outside coastal waters and our sites are north of their 

published range boundary (Wrangell, Alaska) (McConnaughey and McConnaughey 1998). We 

did, however, capture shiner perch at one of our northern outside sites (St. John Baptist Bay-Site 

13; Fig. 1), extending the northern range of this species about 90 km. 

The patchy distribution and variable abundance of many species, and the wide range in 

physical characteristics among individual sites, highlight the importance of site-specific 

evaluation by resource managers. No two eelgrass or kelp sites were identical; subtle differences 

in temperature, salinity, eelgrass shoot density, and exposure to adverse weather among sites can 

influence fish assemblages and abundance. Additionally, our sampling was limited to summer 

and needs to be expanded to other seasons of the year to gain a full understanding of the 

importance of submerged vegetation as fish habitat. 

Eelgrass and kelp are widely distributed in southeastern Alaska and support high species 

richness, diversity, and fish abundance. Our results show that juveniles of many commercially 

important species use these habitats in summer. Eelgrass often occurs in discrete patches, and 

some of these discrete areas may be “essential” for rearing or spawning. Vegetated habitats on or 

near the outer coast may be particularly important to some species of rockfish as nursery areas. 

Similarly, herring may use eelgrass as a spawning substrate in discrete areas, and loss of this 
17


habitat could affect herring populations. Further studies are needed to identify the spatial 

coverage of eelgrass and kelp in Alaska and the function of these habitats as EFH. Information 

from this study on the distribution and habitat of nearshore fish assemblages will help resource 

managers identify and protect coastal areas at risk to human disturbance. 

ACKNOWLEDGMENTS 

We thank Mike Byerly of the Alaska Department of Fish and Game for help with field work. 

We also thank the command and crew of the NOAA ship John N. Cobb for transporting scientists 

and gear to most study locations. This project was funded by the Essential Fish Habitat Task at the 

Auke Bay Laboratory. 
18 

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Table 1.--Mean catch per seine haul and total catch offish in eelgrass (Zostera marina) and kelp (mostly 
 Lamina

habitats at 30 sites in southeastern Alaska from 1998 to 2000. Sampling was between June and August 

Seine hauls totaled 56 in eelgrass and 46 in kelp. Species are listed in decreasing order of abundance b

catch. An asterisk indicates that the species is included in a fishery management plan in Alaska. 

Mean Catch Per Haul Total Cat

Common Name Scientific Name Eelgrass Kelp Eelgrass 

Pacific herring Clupea pallasi 109. 437. 107 

Shiner perch Cymatogaster aggregata 144. 29. 097 

Crescent gunnel * Pho/is laeta 34. 11.07 956 

Chum salmon * Oncorhynchus keta 46. 322 

Pacific sand lance Ammodytes hexapterus 19. 15. 069 

Threespine stickleback Gasterosteus aculeatus 29. 633 

Bay pipefish Syngnathus leptorhynchus 23 Al 0.24 311 

Snake prickleback* Lumpenus sagitta 14. 832 

Tube-snout Aulorhynchus flavidus 11.75 658 

Pink salmon * Oncorhynchus gorbuscha 12. 

Pacific staghom sculpin Leptocottus armatus 439 

Walleye pollock* Theragra chalcogramma 235 

Juvenile greenling Hexagrammos spp. 267 
Table 1 (cont)--

Mean Catch Per Haul Total Cat

Common Name Scientific Name Eelgrass Kelp Eelgrass 

Northern sculpin Icelinus borealis 308 

Tubenose poacher Pallasina barbata aix 324 

Coho salmon * Oncorhynchus kisutch 1.61 259 

Pacific cod * Gadus macrocephalus 190 

Copper rockfish * Sebastes caurinus 187 

Great sculpin * Myoxocephalus polyacanthocephalus 1.07 130 

Silverspotted sculpin Blepsias cirrhosus 1.70 1.07 

Black rockfish Sebastes melanops 1.52 

Kelp greenling H exagrammos decagrammus 1.07 

Whitespotted greenling H exagrammos stelleri 1.14 

Brown rockfish Sebastes auriculatus Buffalo sculpin Enophrys bison 0.41 

Lingcod Ophiodon elongatus 

Arctic shanny Stichaeus punctatus 0.29 0.46 

Kelp perch Brachyistius frenatus 0.13 Rock sole Lepidopsetta bilineata 

Red Irish lord * Hemilepidotus hemilepidotus 
Table 1 (cont)--

Mean Catch Per Haul Total Cat

Common Name Scientific Name Eelgrass Kelp Eelgrass 

Tadpole sculpin Psychrolutes paradoxus 

Rock greenling Hexagrammos lagocephalus Dolly Varden Salvelinus malma Pacific sanddab Citharichthys sordidus Blackeye goby Coryphopterus nicholsi Dusky rockfish * Sebastes ciliatus Masked greenling H exagrammos octogrammus 0.20 

Surf smelt* Hypomesus pretiosus 

Cutthroat trout Oncorhynchus clarki 

Y ellowfin sole Limanda asper 

Sailfin sculpin N autichthys oculofasciatus 

Quillback rockfish * Sebastes maliger 

Brown Irish lord Hemilepidotus spinosus 

Cabezon Scorpaenichthys marmoratus 

Painted greenling Oxylebius pictus Penpoint gunnel * Apodichthys flavidus 

Tidepool snailfish Liparis florae 
Table 1 (cont. )-­

Mean Catch Per Haul Total Cat

Common Name Scientific Name Eelgrass Kelp Eelgrass 

Starry flounder Platichthys stellatus 

Y ellowtail rockfish * Sebastes flavidus 

English sole Parophrys vetulus Pacific tomcod Microgadus proximus 

Butter sole Isopsetta isolepis Pacific sandfish * Trichodon trichodon 

Northern ronquil Ronquilus jordani 

Smoothhead sculpin Artedius lateralis 

Total , 934 
Table 2. Habitat type and capture locations of species included in a fishery management plan (FMP) in Alaska. 

on fish collected by beach seine at 30 sites throughout southeastern Alaska from 1998 to 2000. Sites w

from June to August each year. Habitat represents the vegetation type (eelgrass Zostera marina 
 or kel

Laminaria saccharina) 
 where most fish were captured (::::-50% of the total catch for each species). See 

Table 3 to match site numbers with site locations and names. 

Capture Locations (site numbers) 

FMP Species Group Habitat Eelgrass Kelp 

Target species 

Walleye pollock eelgrass , 17 , 19 

Pacific cod eelgrass , 5 , 7 , 16 , 18 26­ , 14 , 18 , 21 , 22

Y ellowfin sole eelgrass , 10 , 17 

Rock sole kelp , 9 , 12 , 14 , 20 , 30 

Starry flounder eelgrass , 20 , 24 

Butter sole eelgrass 

English sole eelgrass , 23 , 30 Copper rockfish eelgrass , 16 , 18 25­ , 29 , 30 , 18 

Quillback rockfish kelp 

Dusky rockfish eelgrass , 18 , 21 
Table 2 (cont. )--

Capture Locations (site numbers) 

FMP Species Group Habitat Eelgrass Kelp 

Y ellowtail rockfish kelp 

Chum salmon kelp , 14 , 29 

Pink salmon kelp , 14 , 14 , 23 

Coho salmon eelgrass , 14 , 20 , 24 , 29 , 14 , 20 , 22 , 

Forage fish 

Arctic shanny kelp 

Crescent gunnel eelgrass 

Penpoint gunnel eelgrass 

Snake prickleback eelgrass 12­ , 18 22­ , 12 , 14 , 19 , 2

Pacific herring kelp , 18 , 19 Pacific sandfish kelp , 24 Pacific sand lance eelgrass , 20 , 26­ , 14 , 18 , 19 , 25 , 2

Surf smelt eelgrass , 20 , 24 

Other species 

Great sculpin eelgrass 22­

Red Irish lord eelgrass , 5 , 18 , 26­ , 6 , 18 
Table 3. Species richness (number of species) and Shannon-Weiner diversity index (H' for fish 

assemblages sampled with a beach seine at 30 sites in southeastern Alaska from 1998 to 

2000. Eelgrass (Zostera marina) and kelp (mostly Laminaria saccharina) habitats were 

sampled from June through August each year. Missing values indicate no data collected. 

Regions are northern inside and outside and southern inside and outside waters. Refer to 

Figure 1 to match site number with location. 

Number of Species Diversity Index 
 (H'

Site Name and Number Eelgrass Kelp Eelgrass Kelp 

Northern Inside 

Bridget Cove (1) 

St. James Bay (2) 17. 1.32 

Auke Bay (3) 1.56 

Funter Bay (4) 12. 11.0 1.95 

N eka Bay (7) 14. 1.55 1.63 

Tenakee Inlet (8) 1.73 

Ushk Bay (9) 13. 1.80 

Sitkoh Bay (10) 14. 1.26 

Hobart Bay (11) 1.38 

Pybus Bay (12) 12. 14. 1.42 1.11 

Cosmos Cove/Kelp Bay (14) 16. 20. 1.89 1.18 

Median 12. 11.0 1.56 1.38 

Northern Outside


Port Althorp (5) 12. 10. 

Yakobi Island (6) 10. 

St. John Baptist Bay (13) 12. 1.81 
Table 3 (cont. )--

Number of Species Diversity Index (H' 

Site Name and Number Eelgrass Kelp Eelgrass Kelp 

Nakwasina Sound (15) 16. 

Katlian Bay (16) 11.0 1.44 

Sitka Sound (18) 20. 19. 1.11 1.14 

Median 12. 10. 1.44 

Southern Inside 

Farragut Bay (17) 12. 1.48 

Port Camden (19) 17. 

Kah Sheets Bay (20) 16. 12. 1.27 1.69 

Exchange Cove (22) 14. 1.36 1.84 

Olive Cove (24) 14. 1.34 

Steamer Bay (25) 12. 1.52 1.52 

Twelvemile Arm (28) 14. 

Median 14. 1.34 1.48 

Southern Outside 

Port Conclusion (21) 11.0 1.49 

Calder Bay/Shakan Bay (23) 13. 11.0 1.74 1.99 

Warm Chuck Inlet (26) 20. 1.80 

Craig/Klawock Inlet (27) 21.0 19. 1.68 

Port San Antonio (29) 22. 12. 1.98 

Bostwick Inlet (30) 18. 1.18 

Median 20. 11.0 1.74 1.98 
33


Figure 1.-- Locations of eelgrass (Zostera marina) and kelp (mostly Laminaria saccharina) sites 

sampled for fish assemblages in southeastern Alaska. Thirty sites were sampled by 

beach seine from 1998 to 2000. Sampling was between June and August each year. 

Dashed line (Frederick Sound) divides northern and southern regions, whereas dotted 

line separates inside from outside waters. See Table 3 to match site number with site 

name. 
34


Figure 2.-- Box and whisker plots of catch per seine haul (all species) in eelgrass (Zostera 

marina) and kelp (mostly Laminaria saccharina) by region in southeastern Alaska. 

Twenty-five eelgrass sites and 20 kelp sites were sampled by beach seine from 1998 to 

2000. Sampling was between June and August each year. Number of sites in each 

region is shown inside most boxes. Regions were northern inside and outside waters 

and southern inside and outside waters. Scale on ordinate is logarithmic. 
35


Figure 3.-- Box and whisker plots of catch per seine haul of forage fish (Pacific herring, Clupea 

pallasi, and sand lance, Ammodytes hexapterus, combined) in eelgrass (Zostera 

marina) and kelp (mostly Laminaria saccharina) by region in southeastern Alaska. 

Twenty-five eelgrass sites and 20 kelp sites were sampled by beach seine from 1998 to 

2000. Sampling was between June and August each year. Number of sites in each 

region is shown inside most boxes. Regions were northern inside and outside waters 

and southern inside and outside waters. Median values are near or at zero when not 

obvious on graphs. Scale on ordinate is logarithmic. 
36


Figure 4.-- Box and whisker plots of catch per seine haul of gadids (Pacific cod, Gadus 

macrocephalus, and walleye pollock, Theragra chalcogramma, combined) in eelgrass 

(Zostera marina) and kelp (mostly Laminaria saccharina) by region in southeastern 

Alaska. Twenty-five eelgrass sites and 20 kelp sites were sampled by beach seine from 

1998 to 2000. Sampling was between June and August each year. Number of sites in 

each region is shown inside most boxes. Regions were northern inside and outside 

waters and southern inside and outside waters. Median values are near or at zero when 

not obvious on graphs. Scale on ordinate is logarithmic. 
37


Figure 5.-- Box and whisker plots of catch per seine haul of juvenile rockfish (Sebastes, six 

species) in eelgrass (Zostera marina) and kelp (mostly Laminaria saccharina) by 

region in southeastern Alaska. Twenty-five eelgrass sites and 20 kelp sites were 

sampled by beach seine from 1998 to 2000. Sampling was between June and August 

each year. Number of sites in each region is shown inside most boxes. Regions were 

northern inside and outside waters and southern inside and outside waters. Median 

values are near or at zero when not obvious on graphs. Scale on ordinate is 

logarithmic. 
38


Figure 6.-- Frequency of occurrence by site of 12 common species of fish captured in eelgrass 

(Zostera marina) and kelp (mostly Laminaria saccharina) in southeastern Alaska. 

For example, crescent gunnels were captured at all eelgrass and kelp sites. Twenty-five 

eelgrass sites and 20 kelp sites were sampled by beach seine from 1998 to 2000. 

Sampling was between June and August each year. 
39


Figure 7.-- Eelgrass (Zostera marina) shoot density (A) and biomass (B), and kelp (mostly 

Laminaria saccharina) biomass (C) from sites sampled for fish assemblages in 

southeastern Alaska from 1998 to 2000. Twenty-five eelgrass sites and 20 kelp sites 

were sampled by beach seine from 1998 to 2000. Sampling was between June and 

August each year. Data are means and ranges; number of sites above bars. 
RECENT TECHNICAL MEMORANDUMS


Copies of this and other NOAA Technical Memorandums are available from the 

National Technical Information Service, 5285 Port Royal Road, Springfield, VA 22167 

(web site: www.ntis.gov). Paper and microfiche copies vary in price. 

AFSC138 PEREZ, M. A. 2003. Compilation of marine mammal incidental take data from the domestic and joint 

venture groundfish fisheries in the U. S. EEZ of the North Pacific, 1989-2001, 145 p. NTIS number 

pending. 

137 MASELKO, J. M., A. C. WERTHEIMER, and J. F. THEDINGA. 2003. Selection and application of a markand-recapture technique for estimating pink salmon escapements, 44 p. NTIS No. PB2003-107101. 

136 BARBEAUX, S. J., and M. W. DORN. 2003. Spatial and temporal analysis of eastern Bering Sea echo 

integration-trawl survey and catch data of walleye pollock, Theragra chalcogramma, for 2001 and 2002, 

34 p. NTIS number pending. 

135 DIETER, B. E., D. A. WION, and R. A. MCCONNAUGHEY. 2003. Mobile fishing gear effects on benthic 

habitats: A bibliography (second edition), 207 p. NTIS number pending. 

134 ROBSON, B. W. (editors). 2002. Fur seal investigations, 2000-2001, 80 p. NTIS No. PB2003-103825. 

133 ANGLISS, R. A., and K. L. LODGE. 2002. Alaska marine mammal stock assessments, 2002, 224 p. 

NTIS PB2003-103793. 

132 DOYLE, M. J.., M. S. BUSBY, J. T. DUFFY-ANDERSON, S. J. PICQUELLE, and A. C. MATARESE. 

2002. Aspects of the early life history of capelin (Mallotus villosus) in the northwestern Gulf of Alaska: A 

historical perspective based on larval collections October 1977- March 1979, 32 p. NTIS No. PB2002-

102535. 

131 SEASE, J. L., and C. J. GUDMUNDSON. 2002. Aerial and land-based surveys of Steller sea lions 

(Eumetopias jubatus) from the western stock in Alaska, June and July 2001 and 2002, 45 p. NTIS No. 

PB2003-102164. 

130 AYDIN, K. Y., V. V. LAPKO, V. I. RADCHENKO, and P. A. LIVINGSTON. 2002. A comparison of the 

eastern and western Bering Sea shelf and slope ecosystems through the use of mass-balance food 

web models, 78 p. NTIS No. PB2003-100518. 

129 FERRERO, R. C., and L. W. FRITZ. 2002. Steller sea lion research coordination: a brief history and 

summary of recent progress, 34 p. NTIS No. PB2002-107912. 

128 WEINBERG, K. L., M. E. WILKINS, F. R. SHAW, and M. ZIMMERMANN. 2002. The 2001 Pacific 

west coast bottom trawl survey of groundfish resources: Estimates of distribution, abundance, and 

length and age composition, 140 p. + Appendices. NTIS No. PB2002-108221. 

127 MARQUETTE, W. M. 2002. Annotated bibliography of the bowhead whale, Balaena mysticetus, 

1767-1983, 325 p. NTIS No. PB2002-108033. 

126 HONKALEHTO, T., W. PATTON, S. DE BLOIS, and N. WILLIAMSON. 2002. Echo integration-trawl 

survey results for walleye pollock (Theragra chalcogramma) on the Bering Sea shelf and slope during 

summer 2000, 66 p. NTIS No. PB2002-104686. 

125 HONKALEHTO, T., N. WILLIAMSON, and S. DE BLOIS. 2002. Echo integration-trawl survey results 

for walleye pollock (Theragra chalcogramma) on the Bering Sea shelf and slope during summer 1999, 

77 p. NTIS No. PB2002-104686.