Prepared for the National Park Service

Marine Benthic Habitat Mapping of the West Arm, Glacier 

Bay National Park and Preserve, Alaska

By Timothy O. Hodson, Guy R. Cochrane, and Ross D. Powell

Pamphlet to accompany

Scientific Investigations Map 3253

2013

U.S. Department of the Interior

U.S. Geological Survey
ii

Contents

Abstract ........................................................................................................................................................................................ 1

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

Setting ...................................................................................................................................................................................... 2

Geology ................................................................................................................................................................................ 3

Temperate Glacimarine Environment................................................................................................................................... 3

Oceanography ...................................................................................................................................................................... 4

Previous Habitat Mapping in Glacier Bay ................................................................................................................................. 4

Coastal and Marine Ecological Classification Standard ........................................................................................................... 5

Data Sources................................................................................................................................................................................ 5

Multibeam Sonar ...................................................................................................................................................................... 5

Groundtruthing Information....................................................................................................................................................... 5

Methodology ................................................................................................................................................................................. 6

Surficial Geology Component................................................................................................................................................... 6

Historical Bathymetric Data .................................................................................................................................................... 10

Geoform Component .............................................................................................................................................................. 11

Water Column Component ..................................................................................................................................................... 12

Sediment Accumulation.......................................................................................................................................................... 14

Results and Discussion .............................................................................................................................................................. 15

Surficial Geology Component................................................................................................................................................. 15

Geoform Component .............................................................................................................................................................. 16

Water Column Component ..................................................................................................................................................... 19

Sediment Accumulation.......................................................................................................................................................... 20

Benthic Habitats ..................................................................................................................................................................... 22

Conclusions ................................................................................................................................................................................ 24

Management Implications........................................................................................................................................................... 25

Acknowledgments ...................................................................................................................................................................... 25

References Cited........................................................................................................................................................................ 25

Figures

1. Location maps for the West Arm relative to (A) Alaska and (B) Glacier Bay..................................................................... 2

2. Map of USGS Video Observations and NOS Grab Samples. ........................................................................................... 7

3. Map of CMECS rugosity classes for the West Arm. .......................................................................................................... 8

4. Map of CMECS slope classes for the West Arm. .............................................................................................................. 9

5. Glacier Bay oceanographic stations ................................................................................................................................ 12

6. Rock drumlins and other streamlined features in Scidmore Inlet. ................................................................................... 13

7. Maps of (A) upper and (B) bottom water column CMECS habitats ................................................................................. 20

8. Map of average annual sediment accumulation rates for 1970 and 1972 to 2009. ......................................................... 21

9. Perspective view and cross section of the morainal bank at the mouth of Tarr Inlet....................................................... 23
iii

Tables

1. CMECS slope classes. .................................................................................................................................................... 10

2. CMECS rugosity classes surveyed within the West Arm................................................................................................. 10

3. CMECS benthic depth zones surveyed within the West Arm. ......................................................................................... 10

4. Substrate distribution for the West Arm. .......................................................................................................................... 16

5. Substrate distribution by depth zone for the West Arm. .................................................................................................. 16

6. Major geoform distribution for the West Arm. .................................................................................................................. 17

7. Percent mud cover versus geoform for the West Arm..................................................................................................... 17

8. Major geoform distribution by depth zone for the West Arm............................................................................................ 18
1

Marine Benthic Habitat Mapping of the West Arm, Glacier 

Bay National Park and Preserve, Alaska

By Timothy O. Hodson, Guy R. Cochrane, and Ross D. Powell

Abstract

Seafloor geology and potential benthic habitats were mapped in West Arm, Glacier Bay National 

Park & Preserve, Alaska, using multibeam sonar, groundtruthed observations, and geological 

interpretations. The West Arm of Glacier Bay is a recently deglaciated fjord system under the influence 

of glacial and paraglacial marine processes. High glacially derived sediment and meltwater fluxes, slope 

instabilities, and variable bathymetry result in a highly dynamic estuarine environment and benthic 

ecosystem. We characterize the fjord seafloor and potential benthic habitats using the recently developed 

Coastal and Marine Ecological Classification Standard (CMECS) by the National Oceanic and 

Atmospheric Administration (NOAA) and NatureServe. Due to the high flux of glacially sourced fines, 

mud is the dominant substrate within the West Arm. Water-column characteristics are addressed using a 

combination of CTD and circulation model results. We also present sediment accumulation data derived 

from differential bathymetry. These data show the West Arm is divided into two contrasting 

environments: a dynamic upper fjord and a relatively static lower fjord. The results of these analyses 

serve as a test of the CMECS classification scheme and as a baseline for ongoing and future mapping 

efforts and correlations between seafloor substrate, benthic habitats, and glacimarine processes. 

Introduction

This study is a bottom-up approach to mapping benthic habitats (see Greene and others, 2007) in 

the West Arm of Glacier Bay National Park & Preserve (fig. 1). Seafloor substrate and morphology are 

characterized so that they may be correlated to and associated with a specific set of benthic conditions 

favorable for local biota. These include commercially and recreationally important species such as king 

crabs (Paralithodes camtschaticus), Tanner crabs (Chionoecetes bairdi), and Pacific halibut 

(Hippoglossus stenolepis) (Mondragon and others, 2007a,b). Seafloor substrates and, therefore, potential 

benthic habitats were mapped at depths ranging from just below the surface to greater than 400 m in the 

deepest fjord basins. The substrate was characterized by using a combination of high-resolution 

multibeam bathymetry and backscatter imagery, numerous groundtruthing sources, and knowledge of 

the local fjord environment. 

The multibeam data used in this study were collected aboard the National Oceanic and 

Atmospheric Administration (NOAA) ship, Fairweather, during NOAA National Ocean Service (NOS)

hydrographic surveys H12140, H12141, and H12142. Additional groundtruthing was conducted using 

camera sled and ROV (remotely operated underwater vehicle) aboard the R/V Steller, cruise S-T3-10-

GB, in September, 2010. Groundtruth transects were selected based on visual inspection of the NOS 

bathymetric and backscatter intensity data. These observations are supplemented with preexisting 

bottom-grab and sediment-core descriptions, available in the Index to Marine and Lacustrine Geological 

Samples database, maintained by the National Geophysical Data Center (NGDC; last accessed in 2012).
2

Figure 1. Location maps for the West Arm relative to (A) Alaska and (B) Glacier Bay.

The multibeam bathymetric and acoustic backscatter data were compiled with additional 

information in an ESRI (2005) Geographic Information System database to create several map products. 

NOAA and NatureServe Coastal and Marine Ecological Classification Standard (CMECS; Madden and 

others, 2008) was used to classify seafloor substrate, potential benthic habitats, water column properties, 

and seafloor geomorphology (Madden and others, 2009). An additional map of modern sediment flux 

measurements using quantitative differential bathymetry is also presented. These maps serve as 

baselines for further research and have implications for park management.

Setting

Glacier Bay National Park & Preserve is located in southeastern Alaska (fig. 1). It is a fjord 

system that bifurcates into two main northern tributaries: the West Arm and Muir Inlet, also known as 

the East Arm. This study focuses on the West Arm, a 58-km-long system of fjords, including Tarr, Johns 

Hopkins, Queen, Reid, and Tidal Inlets, which have recently undergone well-documented rapid 

deglaciation (Powell, 1984; Hall and others, 1995). The West Arm is a highly dynamic estuarine 

environment owing to its recent deglaciation, high sedimentation rates, and vigorous tidal currents—

forces that affect seafloor stability and constantly shape benthic environments. This diverse settings is 
3

also host to productive food webs; recreational, commercial, and subsistence fisheries; large populations 

of marine mammals and seabirds; and vessel-based tourism (Piatt and Gende, 2007).

Geology 

Glacier Bay is surrounded by three large mountain ranges—the Chilkat Range to the east, the 

Takhinsha Mountains in the north, and the Fairweather Range to the west—that separate the fjord 

system from the Gulf of Alaska. The park is set in a tectonically active area with several nearby active 

fault systems including the Chilkat-Chatham Strait Fault to the east, the Queen Charlotte-Fairweather 

Fault to the west, and the Border Ranges Fault that runs through parts of the West Arm (Powell, 1984). 

Upper Glacier Bay is undergoing glacial isostatic uplift at a rate of 25 mm/yr due to post-Little Ice Age 

ice loss (Larson and others, 2004). The regional bedrock geology is complex, with a range of rock types 

and origins, including metasedimentary rocks intruded by younger granitic plutons. Geological units 

exposed at the surface surrounding the West Arm are predominately Tertiary and Cretaceous granite; 

granodiorite and diorite; Cretaceous, Silurian, Devonian, and Permian metasedimentary rocks; and 

Quaternary sediment (Powell, 1984).

Temperate Glacimarine Environment

The cool to temperate maritime climate of southeast Alaska and very high, tectonically active 

mountain ranges permit widespread glaciation at a relatively low latitude (Wilson and Overland, 1987). 

Abundant precipitation in the form of snow in the surrounding mountain ranges feeds many valley 

glaciers that flow into Glacier Bay that are among the largest and most active in southeast Alaska. The 

glaciers of this region are temperate and characterized by seasonally abundant meltwater that carries 

high sediment loads to produce large depositional landforms (for example, Goldwait, 1974; Powell, 

1991; Hunter, 1994). Significant research has focused on the rich glacimarine sedimentary record within 

Glacier Bay, yielding insight into complex glacimarine processes (for example, Powell, 1991; Hunter 

and others, 1996; Cowan and others, 1999) and the history and processes of deglaciation (Seramur and 

others, 1997).

Glacial sediment fluxes from the temperate glaciers in southeast Alaska are among the highest 

recorded worldwide (Powell and Molnia, 1989; Hallet and others, 1996; Elverhøi and others, 1998). 

Extreme rates of sediment accumulation, in some instances in excess of 80 m/yr, have been documented 

near glacial termini in the region (Powell, 1991; Hunter and others, 1996; Cai and others, 1997; Seramur 

and others, 1997) and decrease very rapidly with distance from the terminus (for example, Syvitski, 

1989). A proper understanding of these rates is important because of their potential paleoclimatic 

significance (Cowan and Powell, 2007) and their affect on glacier stability (Powell, 1991) and also 

because such high clastic sedimentation may be a major physical control on the diversity and spatial 

distribution of fjord biota (for example, Carney and others, 1999; Wlodarska-Kowalczuk and Pearson, 

2004). 

The post-Little Ice Age deglaciation in the region has occurred at some of the highest rates 

documented worldwide. Nearly 100 km of glacier retreat during the past two centuries has left behind a 

network of canals, moraines, outwash complexes, and large volumes of glacimarine sediment. Prior to 

1860, the glaciers of the West Arm and Muir Inlet formed a confluent tidewater glacier complex near 

Tlingit Point. From 1860 to 1892, the ice front receded rapidly by at least 1.8 km/yr, dividing into two 

distinct fronts near the junction of Tarr and Johns Hopkins Inlets sometime between 1879 and 1892 

(Cai, 1994). By the late 1920s, the ice fronts terminated roughly 2 km upfjord from their modern 

positions. The retreat of Johns Hopkins Glacier ended by about 1926. In Tarr Inlet, the retreat of Grand 

Pacific Glacier continued until the early 1940s. Since that time, the termini of the West Arm glaciers 

have been advancing or quasi-stable (Hall and others, 1995; Powell, 1984; Powell, 1991), fluctuating 
4

asynchronously, apparently controlled by autogenic factors such as glacier dynamics and channel 

geometry rather than climate (Powell, 1984, 1991).

Oceanography

The oceanographic setting of Glacier Bay is also complex, owing to the concurrence of 

bathymetric variability, tidal currents, and strong seasonal stratification resulting from high rates of 

glacial ablation, snow melt, and precipitation (Hooge and Hooge, 2002; Etherington and others, 2007a). 

The morphology of the West Arm is characteristic of a glacial fjord and includes a shallow sill topped 

with a glacial morainal bank complex at its mouth (Seramur and others, 1997), steeply sloping walls up 

to 77°, and multiple deep basins separated by transverse sills and morainal banks. 

Areas of shallow bathymetry influence tidal current velocity and vertical mixing (Etherington 

and others, 2007a). In contrast, deep basins are highly stratified in the pelagic environment and have 

minimal benthic currents. Average root mean square (RMS) current speeds (derived from an advanced 

circulation, or ADCIRC, tidal circulation model) for the main stem of the West Arm are small, ranging 

from 0.001 to 0.043 m/s. However, peak instantaneous velocities are approximately 50 to 100 percent 

higher than RMS velocity values, particularly over areas of shallow bathymetry (Etherington and others, 

2007a; Hill, 2007). Model results demonstrate the large tidal range within Glacier Bay, with values 

averaging 3.86 m at the lowest portions of the Bay, increasing with distance up the arms of the Bay, and 

reaching an average of 4.59 m at the head of the inlets (Hill, 2007; Etherington and others, 2007a). The 

highest tides in the Bay are found in Adams Inlet (Hill, 2007). Glacier Bay exhibits mixed tides, with 

two high and two low tides per day and with successive high and low tides of varied amplitude 

(Etherington and others, 2007a).

Freshwater input at the head of the fjord is a dominant driver of water-column stratification 

(Etherington and others, 2007a). Spatial and seasonal variability are greatest for salinity and 

stratification and are directly associated with freshwater flux (Etherington and others, 2007a; Hill and 

others, 2009). This flux peaks between June and October at about 1,000 m3

/s for the entire Glacier Bay 

watershed (Hill and others, 2009). The summer discharge peak coincides with peak stratification, peak 

water temperature, minimum surface salinity, and generally higher chlorophyll a concentrations 

(Etherington and others, 2007a). Likewise, peak glacimarine sediment flux also occurs during the 

summer months due to enhanced subglacial stream discharge (Cowan and Powell, 1990).

Freshwater flux from glacial ablation is both important to local fjord conditions (Etherington and 

others, 2007a; Hill and others, 2009) and globally, because the glaciers of southeast Alaska account for 

15 percent of present-day eustatic sea level rise (Meier and others, 2007). The thinning of southeast 

Alaskan glaciers contributed 0.04±0.01 mm/yr to global sea-level rise in the latter part of the 20th

century (Larson and others, 2007). More recently, mass loss from these glaciers was found to contribute 

0.23±0.01 mm/yr to global sea-level rise for the period April 2003 through March 2007 (Luthcke and 

others, 2008).

Previous Habitat Mapping in Glacier Bay

Several benthic habitat mapping initiatives have been completed in Glacier Bay proper. In 2001, 

the U.S. Geological Survey (USGS) collected multibeam bathymetry for this area (Carlson and others, 

2002). In 2004, ground-truth-data were collected to supervise an effort to correlate seafloor geology and 

biology. This work included seafloor video observations and sediment sampling and resulted in a 

characterization of seafloor morphology, substrate, and habitat distribution following the Greene and 

others (1999) classification scheme (Harney and others, 2007). 

Subsequent research based on these data includes a geological to biological association analysis 

by Etherington and others (2007b). This work used detrended correspondence analysis, a multivariate 
5

statistical technique, to examine relations between habitat types and taxa distribution. Etherington and 

others (2007b) found substrate type and current exposure to be the dominant control on species 

distributions in Glacier Bay. Three benthic habitats were identified: (1) shallow-water, high-current sand 

and cobble habitat associated with urchin, horse mussel, and scallop; (2) deep-water mud habitat 

associated with gastropod, algae, flatfish, Tanner crab, shrimp, sea pen, and other crustaceans; and (3) 

moderate-depth cobble and mud habitat associated with sea star, rockfish, sculpin, anemone, sea 

cucumber, worm, pollock/cod, basket star, and other fish (Etherington and others, 2007b). 

The pilot study for the project, undertaken by Trusel and others (2010), mapped seafloor geology 

in Muir Inlet, relating factors such as water depth, glacial proximity, and seafloor morphology with the 

spatial and temporal distribution of benthic habitats.

Coastal and Marine Ecological Classification Standard

The Coastal and Marine Ecological Classification Standard (CMECS), developed by NOAA and 

NatureServe, was proposed as a national standard for classification of coastal and marine resources, 

adhering to the Federal Geographic Data Committee (FGDC) in 2008. CMECS encompasses five 

individual components to cover all aspects of the marine environment: surficial geology, water column, 

geoform, sub-benthic, and biotic cover. Results presented here focus on the surficial geology component 

and the geoform component but also include preliminary application of the water column component 

and adhere to the guidelines of CMECS Version III (August 2009 draft version, Madden and others, 

2009). The surficial geology component (SFG), the primary component, is a hierarchical scale-based 

system that describes geomorphological, physico-chemical, and biological compositions of the coastal 

and marine substrates (Madden and others, 2009). The water column component (WCC) describes the 

structure, processes, and biology of the water column. The geoform component (GFC) describes the 

coastal seafloor geomorphology at different scales (Madden and others, 2009). 

Data Sources

Multibeam Sonar

Benthic habitat and seafloor substrate mapping for the West Arm were conducted using 

multibeam sonar data collected onboard the NOAA ship, Fairweather, during NOAA NOS 

hydrographic surveys H12140, H12141, and H12142 in late September through early November 2010. 

The Fairweather employed A Reson 7111 multibeam for the purpose of high-resolution bathymetric 

surveying. Data were processed using CARIS HIPS & SIPS v 7.0, Service Pack 1, Hotfix 5, cleaned for 

errant points, referenced to mean lower low water (MLLW) by correcting for tide, and finally 

transformed into depth versus absolute position. MLLW was locally determined by tide stations installed 

at Composite Island and Tarr Inlet. The operating National Water Level Observation Network 

(NWLON) primary tide station at Elfin Cove, AK (945–2634), served as control for datum 

determination (NOAA 2009a,b,c). For a more detailed discussion of data processing/acquisition and 

quality control procedures, refer to the descriptive reports that accompany each survey or NOAA ship, 

Fairweather, 2009 Data Acquisition and Processing Report (DAPR). Bathymetry and backscatter data 

were gridded using 16-m horizontal grid resolutions. About 381 km2 or 93 percent of the West Arm is 

covered by bathymetric data, extending from just below sea level to over 400 m depth in the lower West 

Arm fjord basin and from Tlingit Point to the heads of Tarr and Johns Hopkins Inlets. 

Groundtruthing Information

Groundtruthing operations were conducted aboard the R/V Steller in late August and early June 

of 2010. USGS seafloor observations, collected via towed video sled, provided the primary ground-truth 
6

source for this study (see cruise report at http://walrus.wr.usgs.gov/infobank/s/st310gb/html/s-t3-10-

gb.meta). Transects were selected to ground truth across the full spectrum of depth, slope, and rugosity 

observed in the multibeam bathymetry. Selection was oriented toward resolving both common and 

unique features of the seafloor and examining regions of transition between different substrate types. 

Video observations were subsequently used to construct maps of substrate type and habitat distribution.

The video sled was equipped with forward- and downward- facing video cameras, lights, an 

altimeter, and a pressure (depth) sensor. Two down-pointing lasers, spaced 20 cm apart, provided scale 

in the seafloor imagery. The sled was towed behind the surface vessel at speeds of 0.5–1.5 kn, generally 

operating at an altitude between 1 and 2 m above the seafloor. Video footage was recorded to digital 

mini-DV tape, which was continuously imprinted with altitude, pitch, roll, water depth, ship latitude and 

longitude, ship speed, ship heading, and Greenwich Mean Time (GMT). Ship position was determined 

by differential geographic positioning system (dGPS). All instrument data were multipexed through a 

sub-sea housing and transmitted by the 12-conductor cable to a topside console.

Real-time seafloor observations were recorded using an X-keys programmable keypad at 1-

minute intervals during each transect following the methodology of Anderson and others (2008). Time 

(GMT), ship position, and other ship data were automatically recorded each time an observation event 

was entered. Positional data in the observation file were later corrected to true sled position, determined 

using a Linkquest Tracklink 1500, which provided sled position relative to the ship-board dGPS. 

Observations at each point included primary and secondary substrate type (for example, mud/mud, 

boulder/cobble), substrate complexity (rugosity), seafloor slope, benthic biomass, the presence of 

benthic organisms and demersal fish, and small-scale sea-floor features (for example, tracks and 

burrows).

In areas of complex bathymetry and substrate, the limited maneuverability granted by the tow 

sled was often insufficient for reliable and continuous data collection. Such transects were completed 

using a Benthos Stingray ROV. Due to the limited range imposed by the 400 umbilical, the ROV 

occupied an auxiliary role during groundtruthing investigations. The buoyancy provided by the Stingray 

platform was inadequate for the equipment of the Tracklink positioning transducer. As a result, ROV 

observations are given with ship position only. Because the ROV was tethered to a clump weight 

lowered beneath the ship, true ROV position is constrained to within ~100 m of the ship's position. 

In addition to the seafloor video transects, 127 bottom-grab samples (available in the NGDC’s 

Index to Marine & Lacustrine Geological Samples—http://www.ngdc.noaa.gov/mgg/curator/), seismicreflection profiles (Cowan and others, 1994; Cai, 1994), and Landsat imagery also aided in the 

interpretation of the multibeam data. In particular, an understanding of modern processes active in the 

glacimarine environment was fundamental to our interpretations, especially in areas of poor coverage.

Methodology

Surficial Geology Component

The classification of seafloor habitats was performed using a supervised manual classification of 

seafloor substrate based on knowledge from groundtruthing sources (fig. 2): two derivative bathymetric 

properties (seafloor rugosity, fig. 3) and slope (fig. 4). Multibeam backscatter supplemented the primary 

data sets in locations where surficial geology was ambiguous. However, due to the low quality of the 

backscatter in the West Arm, we were unable to replicate the approach employed in Muir Inlet, where 

backscatter intensity was used to infer substrate distribution (see Trusel and others, 2010). Instead, our 

approach relies heavily on groundtruthed data collected during this study and previous NOS cruises. 

Seafloor rugosity (fig. 3) was calculated using IVS 3-D Fledermaus. Rugosity is a dimensionless 

measure of seafloor roughness or its actual surface area divided by its planar area. Therefore, a 
7

completely flat surface has a rugosity of exactly 1. In general, a higher rugosity is characteristic of rough 

substrates such as rocky areas. Likewise, lower rugosity is characteristic of flat, less complex, softbottom substrates. The second derivative bathymetric measurement is seafloor slope (fig. 4). Because of 

sediment instability on steep slopes, areas with very high slope are often consolidated glacial material or 

bedrock, whereas low sloping areas are the loci of soft-sediment deposition and redeposition from slope 

failures and sediment gravity flows from fjord walls. 

Figure 2. Map of USGS Video Observations and NOS Grab Samples.
8

Figure 3. Map of CMECS rugosity classes for the West Arm.
9

Figure 4. Map of CMECS slope classes for the West Arm.
10

Rugosity and slope rasters were both reclassified into groups according to CMECS such that 

areas with similar rugosity or slope are combined into classes (figs. 3, 4). Rugosity is a somewhat 

qualitative measurement that is biased based on the resolution of the bathymetry, that is, a rugosity value 

obtained with 16-m

2 resolution will be different for the same area using 5-m2 bathymetry data. 

Therefore, rugosity classes may be altered in specific applications to better represent the data (for 

example, Greene and others, 2007). We chose to modify the CMECS classes to better represent 

variability within our rugosity measurements (tables 1–3).

Historical Bathymetric Data

Two historical bathymetric datasets were used to measure recent sediment accumulation within 

the West Arm. NOAA NOS hydrographic surveys H09315 and H09316, collected in August 1972 

aboard the NOAA ship, MacArthur, cover Johns Hopkins and Tarr Inlet respectively (NOAA 1972a,b). 

Table 1. CMECS slope classes.

Slope Vertical angle1 Percentage of 

total area Area (km2)

Flat 0–5° 41.4 159.2

Sloping 5–30° 51.5 197.9

Steeply sloping 30–45° 5.4 20.8

Vertical 45–90° 1.7 6.4

Overhang1 >90° 0 0

1 The greatest slope measured in the West Arm was 72.8°.

Table 2. CMECS rugosity classes surveyed within the West Arm.

Rugosity types Values1 Percentage of 

total area Area (km2) 

Very Low 1–1.25 94.4 356

Low 1.25–1.5 3.4 12.8

Moderate 1.5–1.75 1.1 4.3

High 1.75–2 1.9 1.9

Very high >2 2.2 2.2

1

Modified rugosity values based on Madden and others (2008) and Greene and others (2007).

Table 3. CMECS benthic depth zones surveyed within the West Arm.

Benthic depth zone

Water depth range

(m below sea 

level)

Percentage of 

total area Area (km2) 

Shallow infralittoral 0–5 0.1 2.3

Deep infralittoral 5–30 7.7 29.6

Circalittoral 30–80 16.2 62

Circalittoral (offshore) 80–200 25.4 97.4

Mesobenthic 200–1,000 50.2 192.5
11

Historical bathymetric data from the lower West Arm and its tributaries were obtained from NOS 

hygrographic surveys H09138, H09139, H09141, H09142, H09143, collected in June through August of 

1970 aboard the NOAA ship, Fairweather (NOAA 1970a,b,c,d,e). Both datasets were collected using 

Raytheon DE-723 fathometers for depth measurements. Sounding velocity corrections were determined 

using serial temperature and salinity. In Johns Hopkins and Tarr Inlets, velocity corrections were less 

than 0.5 percent of the sounding depth for the entire survey area and, therefore, velocity corrections 

were not applied to surveys H09315 and H09316 (NOAA 1972a,b). Depth measurements were corrected 

for tidal state and referenced to MLLW. Locations were determined using visual three-point sextant fix 

methods. Hydrographic signal positions were established using a WANG Model 700 Calculator in 

conjunction with the WANG Geodetic Program Library (NOAA 1972a,b). 

A preliminary surficial geologic map was constructed using a maximum likelihood classification 

(MLC) based on slope, geoform, and groundtruthing observations. Our approach relies on the 

assumption that geoform and slope (angle of repose) are often indicative of substrate; the primary caveat 

is that a feature may be draped in one sediment type, while the morphology is inherited from the 

underlying material (for example, mud draping a steep bedrock outcrop). To reduce misclassification by 

the MLC, the possible substrate types were initially limited to two general induration classes: rock 

bottom and unconsolidated bottom. The resulting map provided the template for subsequent manual 

classification. Flat to sloping areas classified as rock bottom were investigated and changed to 

unconsolidated bottom when supported by ancillary data or geological reasoning. Similarly, steeply 

sloping and vertical areas classified as unconsolidated bottom were reclassified to rock bottom if 

reasonable.

Further classification was completed in the surficial geology component down to the subclass 

level, where unconsolidated bottom was divided into mud, sand, mixed sediments, and cobble/gravel. 

Rock bottom was further divided into bedrock and boulder/rubble. Considering the extreme 

predominance of glacimarine sedimentation in the West Arm and groundtruthing that confirmed 

substrates dominated by mud (silt and clay) for all basin floor areas, the unconsolidated bottom class 

was first characterized as entirely mud. We assume most areas in the West Arm are veiled in mud, an 

inference supported by groundtruthing data. Lacking abundant physical samples or imagery of any soft 

bottom material other than mud, geological reasoning was used to classify other unconsolidated bottom 

subclasses. Numerous side-input fluvial sources enter the West Arm and often manifest in fjord-edge 

deltas. Transport channels on the delta slopes are evident in the backscatter as having a higher intensity 

relative to the surrounding cover. We assume most of these deltaic sources transport sand-sized particles 

into the fjord although samples are lacking for many locations, and thus these areas were typically 

classified using the CMECS sand subclass. Notable exceptions to this rule of thumb include Johns 

Hopkins and Tidal Inlets, where the steep topography introduces larger clasts into the deltaic 

environment. Such areas were classified as either cobble/gravel or unclassified soft bottom depending on 

the availability of groundtruthed observations. The sand subclass was also applied to active morainal 

banks. In this environment, the turbidity of the water column limited the effectiveness of video 

observation. While processes such as dumping and gravity flows contribute coarser sediments near the 

terminus, studies of temperate glacimarine environments (Cai, 1994; Hunter, 1994) suggest that the 

morainal core still falls within the CMECS definition of the sand subclass. In subclassifying the rock 

bottom class, all areas were initially assumed to be bedrock. Bedrock areas were groundtruthed using 

seafloor observations (this study), seismic reflection data (Cai, 1994), or observation of transitions of 

subaerially exposed steep bedrock cliffs into the submarine environment. Areas of apparent submarine 

talus were identified through fine scale investigation and classified as boulder/rubble (fig. 5). Most 

commonly, boulder/rubble exists at the base of submarine bedrock cliffs and is characterized by a lower 

slope than the bedrock and a lobate, splay geometry. These are inferred to form from rock falls and 

slides that originate both above and below water.
12

Figure 5. Glacier Bay oceanographic stations (Trusel and others, 2010, adapted from Etherington and others, 

2007a).

Geoform Component

Geoforms in the West Arm were manually selected from the multibeam bathymetry data with the 

aid of video observations, knowledge of glacimarine processes, well-documented glacial history in the 

West Arm, and interpretations from other studies (for example, Cai, 1994). Spatial scales defined within 

the CMECS framework were used to define linear scales using the largest measurable axis. Geoforms 

were only characterized down to the mesogeoform level (tens of meters to kilometers in size) because of 

the limited resolution of our bathymetric data. Many areas in the West Arm fit into more than one 

megageoform and mesogeoform class. For example, the West Arm lies within the continental margin 

megageoform, but it is also a fjord megageoform. At the mesogeoform level, a fjord wall is a 

mesogeoform, but the wall also has multiple mesogeoform-scale bedrock outcrops and other features. 

Therefore, when delineating polygons, it was necessary to have multiple megageoform and 

mesogeoform categories. These are listed in the GIS table as “MEGA_GF”, “MEGA_GF_2”, and so 

forth. While multiple geoforms were selected for each spatial scale, a primary and most informative 

geoform was chosen for display at each scale; these are listed in the GIS table as “DISPMEGAGF” and 

“DISPMESOGF”. Because all smaller geoforms lie within the fjord megageoform, the primary 

mesogeoform is shown in sheets 3 and 4. The CMECS benthic depth zones divide many of these 

mesogeoforms. To aid in visualization, the color shade of each geoform type gets darker as depth zone 

increases.

Water Column Component

Following the CMECS system, water-column classes and attributes were assigned to locations of 

established oceanographic stations within Glacier Bay (Etherington and others, 2007a). Two main data 
13

sets were used to define classes and attributes: (1) conductivity temperature depth (CTD) data 

(Etherington and others, 2007a) and (2) results from a tidal circulation model (Hill and others, 2009; 

Hill, 2007). Results of the tidal circulation model were used to classify the CMECS attributes of tidal 

range and energy intensity, whereas the CTD data were used for all other water-column attributes. 

Model predictions of water elevation have been validated against several NOAA stations within Glacier 

Bay and resulted in strong agreement between predicted and measured values. Model predictions of tidal 

velocity have been compared with minimum and maximum values of velocity at several NOAA stations 

within Glacier Bay, and the model showed general agreement.

CTD data were collected at 22 stations spanning the axes of Glacier Bay from 1993 to 2002 and 

covering all seasons (fig. 6). Parameters include salinity, temperature, density/stratification, turbidity, 

photosynthetically available radiation, and chlorophyll a. This set of eight stations (6–12 and 21) spans 

the length of the West Arm's mainstem through Tarr Inlet. Detailed computational tidal simulations of 

Glacier Bay were conducted using an ADCIRC tidal circulation model (Hill, 2007; Hill and others, 

2009). ADCIRC output includes time series and global output of water-surface elevation and depthintegrated velocity. To determine a single representative value of tidal-current speed and tidal range at 

each oceanographic station, the RMS values of speed and tidal elevation were calculated from the results 

of a harmonic analysis of the model domain (Hill, 2007). 

The framework for the CMECS water column component is in draft form and additional work is 

needed to refine it and develop the rules for combining classifiers to identify and describe the water 

column units (Madden and others, 2008). As a result, this study will employ the approach developed for 

habitat mapping in neighboring Muir Inlet (Trusel and others, 2010). The structure of the water column 

was used to define two vertical strata—upper water layer and bottom water layer—which are defined by 

those strata above and below the pycnocline, respectively. The pycnocline within Glacier Bay varies 

both spatially and temporally but generally exists at 15 m depth or shallower. Because temporal 

averages were used to define the water-column properties and to simplify the classification of water 

layers, the upper water layer was defined as 0–15 m below the surface while the bottom water layer was 

the remaining water column below this stratum. This standard definition was used for all oceanographic 

stations of Glacier Bay, and average oceanographic parameter values from 0 to 15 m were used to 

classify the upper water layer.

CMECS water-column classes and general attributes were applied to the upper water column and 

bottom water column separately for each of the oceanographic stations. All attributes that contained data 

Figure 6. Rock drumlins and other streamlined features in Scidmore Inlet.
14

were assessed and classified. Averages of parameters over tidal conditions (for example, ebb/flood, 

spring/neap) and various time scales (months, years) were used to classify each oceanographic station. 

The output of tidal velocity from the tidal circulation model is used to classify energy intensity in the 

upper water column. In shallower areas where vertical mixing is apparent and tidal energy is higher

(Etherington and others, 2007a; Hill and others, 2009), bottom energy intensity is assumed to mirror 

surface energy intensity, and depth-integrated velocity values are used to also classify energy intensity 

in the bottom water-column stratum. In deeper areas where stratification is higher and tidal energy is 

lower (Etherington and others, 2007a; Hill and others, 2009), energy intensity within the bottom water 

column-stratum is classified as no energy. Visual observations of virtually no current motion and 

accumulation of fine sediments in these deeper areas support this assumption (Etherington and others, 

2007b; Harney and others, 2007). Values were only assigned to a point location and were not 

extrapolated beyond the oceanographic station; thus, only the central regions of the inlets of Glacier Bay 

were classified. Therefore, the water-column classification differs from the geoform and benthic cover 

classifications, which were based on a comprehensive continuous data set covering almost the entirety 

of the West Arm.

Sediment Accumulation

Sediment accumulation rates for most of the West Arm were calculated using quantitative 

differential bathymetry. Three bathymetric datasets were used: the 2009 multibeam bathymetry used in 

this study for seafloor characterization and the 1970 and 1972 singlebeam bathymetry from NOAA NOS 

hydrographic surveys. Average sediment accumulation rates were calculated by subtracting the depths 

from 2009 from those measured in 1970/72 and then dividing by the time period. For this study we are 

interested in modern sedimentation rates because of their potential as a limiting factor in the distribution 

and diversity of benthic biota (for example, Carney and others, 1999; Wlodarska-Kowalczuk and 

Pearson, 2004).

Because poor between-track spatial resolution is often associated with the singlebeam collection 

methods in the NOS data, the historical bathymetric data points were manually modified to artificially 

increase fjord basin-edge resolution. While geographic locations of the historical soundings are 

potentially highly accurate (see Umbach, 1976), even minor errors in horizontal location over variablerelief bathymetry can lead to large errors in depth measurement. This potentially problematic scenario is 

avoided by making measurements only over the very low relief and slope basin floor areas, where poor 

between-track data coverage is not critical.

The 1970 and 1972 bathymetric grids were differenced with the 2009 multibeam bathymetry 

using ArcGIS over the low relief and low rugosity fjord-floor areas. In general, basin floor areas were 

delineated as having a slope of less than 5°. The resulting sediment-thickness grid was divided by 39 

and 37 years (1970 to 2009 and 1972 to 2009, respectively) to calculate an average annual sediment 

accumulation rate between elapsed surveys.

We assume that the flat fjord floor character has remained relatively constant and that the 

primary temporal change has been basin-floor aggradation. This assumption is supported by seismic 

profiles showing thick and continuously well-stratified glacimarine sediment horizons in the deep basins 

of the West Arm that onlap adjacent walls and bathymetric highs (for example, Cai, 1994; Cowan and 

others, 1999). We also assume that the bulk of sediment accumulation occurs in the fjord-floor basins, 

either through direct deposition from glacimarine suspension settling or through redepositional events 

from slope failures, sediment gravity flows, and other mass movements, processes common to fjords 

(for example, Powell and Molnia, 1989; Syvitski, 1989). Using these two assumptions, we have 

modified the results of the differential bathymetry analysis by extrapolating the resulting sedimentation 

rates to the edges of the fjord-floor basins as defined in the 2009 multibeam data. These modified data 
15

were interpolated and gridded using the natural neighbor interpolation function within ArcGIS. In effect, 

this method simply extrapolates from the relatively accurate data in each basin, reducing the affect of 

erroneous soundings. The result is a relatively planar surface that mirrors the basin floor morphology.

Results and Discussion

Surficial Geology Component

Results of the subclass level SGC mapping for the West Arm are shown in sheets 1 and 2. 

Coverage for the SGC substrate classification is summarized for the entire fjord (table 4). As expected, 

unconsolidated bottom types dominate the West Arm, owing to the large glacimarine sediment flux from 

Tarr and Johns Hopkins Inlets. Seventy-two percent of the West Arm is covered by mud, far more than 

any other bottom type. The second most abundant substrate in the West Arm is unclassified 

unconsolidated bottom, which composes about 14 percent of mapped substrate. The more general 

unconsolidated bottom class was typically applied where groundtruthing coverage was poor but higher 

energy processes, such as tidal winnowing, are suspected to disrupt hemipelagic sedimentation. 

Prominent examples include the shallows of Hugh Miller Inlet and along many of the steep fjord walls. 

The latter environment falls under the influence of gravity flows and rock falls rather than tidal 

winnowing. The sand subclass covers 3.0 percent and typifies the foresets of side-wall and fjord-head 

deltas and active morainal banks. The latter environment likely includes a large component of other size 

fractions that reflect processes, including dumping and gravity flows (Hunter, 1994), yet still conforms 

to the CMECS definition of the sand subclass. Areas where no single size fraction constituted the 

majority of the substrate fall under the mixed sediments subclass. Mixed sediments, composing 1.6 

percent of the West Arm, are primarily found in the shallows of Hugh Miller Inlet and at the mouth of 

Tidal Inlet, where winnowing has exposed ice-contact sediments deposited during the post-Little Ice 

Age retreat of the Russell System. Of the two rock bottom subclasses, bedrock is the most abundant, 

constituting 7 percent of the West Arm and 98 percent of the rock bottom class. Boulder/rubble could be 

confidently mapped in only 0.2 percent of the study area. This disparity may be partially attributable to 

the distribution of observation points, as steep fjord walls posed a significant hazard to groundtruthing 

operations in shallow water. Such environments are suspected of having a significant boulder/rubble 

component owing to the combination of rock falls and current winnowing. The true abundance of the 

boulder/rubble substrate likely falls within one order of magnitude of the value presented in table 4, 

which constitute <2 percent of the West Arm.

The summary of substrates for each CMECS depth zone illustrates the types of benthic habitats 

available at different depths within the West Arm (table 5). The majority of rock bottom substrates are 

located in the circalittoral (offshore) and mesobenthic depth zones. This is expected, because the fjord 

walls are predominantly located within these depth zones (table 5). Likewise, the vast majority of mud 

falls within the mesobenthic depth zone, which is dominated by fjord basin floors. Despite the inherent 

relation between mud and the fjord floor class, a large discrepancy exists between their abundances, 

roughly 72 percent and 34 percent, respectively, attributed to the fact that hemipelagic sediment tends to 

drape low energy environments, regardless of the underlying geoform. Shallower, higher energy 

environments, where the finer hemipelagic component is winnowed out, are more typically associated 

with the mixed sediments and unclassified unconsolidated bottom classes. The relative distribution of 

these substrates reflects this, exhibiting the greatest abundances in the depth zones above 200 m. The 

26.8 km2 of mixed and unclassified sediments found within the circalittoral (offshore) and mesobenthic 

zones (80–1,000 m) are suspect and may, in fact, be dominated by mud. In general, the application of 

these classes within the deeper depth zones was reserved for sites where the substrate is suspected of 

varying temporally, such as at lower delta forsets and proximal to steep bedrock cliffs. In the former 
16

Table 4. Substrate distribution for the West Arm.

CMECS class CMECS subclass Percentage of 

total area Area (km2)

Unconsolidated 

Bottom

Unclassified 14.4 55.4

Mud 72.0 276.6

Sand 3.0 11.8

Mixed sediments 1.6 6.2

Cobble/gravel 1.7 6.5

Rock bottom Boulder/rubble 0.2 0.6

Bedrock 7.0 26.7

Table 5. Substrate distribution by depth zone for the West Arm.

Shallow infralittoral:

0–5 m water depth

Deep infralittoral:

5–30 m water depth

Circalittoral:

30–80 m water 

depth

Circalittoral 

(offshore):

80–200 m water 

depth

Mesobenthic:

200–1,000 m water 

depth

CMECS

Subclass Percent Area (km2) Percent Area (km2) Percent Area (km2) Percent Area (km2) Percent Area (km2)

Unclassified 

soft-bottom

0.3 1 3.9 15 4.1 15.9 3.4 13.1 2.6 10

Mud 0 0 2.1 8.1 9.3 35.8 17.5 67.3 43 165.2

Sand 0 0.1 0.5 2 0.7 2.8 1.0 3.9 0.7 2.9

Mixed 0 0 0.2 0.8 0.4 1.6 0.7 2.5 0.3 1.2

Cobble/

gravel

0.1 0.3 0.5 1.9 0.2 0.8 0.3 1.1 0.6 2.4

Boulder/

rubble

0 0 0 0.1 0.1 0.3 0.0 0.2 0 0

Bedrock 0 0 0.4 1.7 1.3 4.9 2.4 9.2 2.8 10.7

environment, variation may be seasonal, reflecting changes in stream discharge and sea-ice cover. In the 

latter, temporal variation is likely less predictable with predominately hemipelagic sedimentation 

punctuated by infrequent and perhaps catastrophic gravity flows and rock falls. Sand and cobble/gravel

subclasses are predominately associated with the delta and fan geoforms, most commonly found in 

shallow nearshore environments. The primary exception occurs along submarine channels where sand 

may be transported into the distal areas of the basin.

Geoform Component

The West Arm lies within the continental margin megageoform and is also a fjord megageoform. 

For simplicity, we characterized geoforms down to the mesogeoform scale (tens of meters to kilometers 

in size). Additionally, the resolution of our data was a limiting factor in geoform characterization. The 

primary mesogeoforms characterized within the West Arm are fjord wall/rock outcrop, floor, delta /fan, 

and moraine geoforms. Minor geoforms include slumps and submarine channels (table 6). The high 

relative proportion of walls, floors, and moraines is expected and is characteristic of glacial fjord 
17

Table 6. Major geoform distribution for the West Arm.

Megageoform Mesogeoform Percentage of total 

area Area (km2)

Fjord Channel 1.8 6.8

Delta/Fan 7.1 27.3

Floor 33.9 130.4

Moraine 29.3 112.5

Slump 0.2 1.0

Wall/Rock Outcrop 27.6 106.2

morphology. Numerous deltas exist along the fjord walls that are both fluvial and glacifluvial in origin, 

with most at least partially fed by glacial meltwater.

While certain geoforms are inherently related to specific substrates (for example, the floor 

geoform and the mud substrate), such associations should be made with caution. For example, rock 

drumlins in Scidmore Bay (fig. 6) are classified with the wall/rock outcrop class, implying that the 

morphology of the feature is bedrock controlled. The surficial sediment, however, consists of a 

heterogeneous mixture of bedrock, gravel, sand, and mud. Similarly many areas classified as moraine 

within the West Arm are partially or entirely draped in mud. In a dynamic environment, geoforms are 

the product of both relict and modern processes. Drawing direct associations between habitat and 

geoform should be done on a case-by-case basis, accounting for local conditions.

Large areas in the vicinity of Hugh Miller Inlet are characterized as moraine using CMECS 

terminology (sheet 3). These features are associated with an interval of quasi-stability and downwasting 

coeval to rapid retreat in the deeper West Arm proper. Upfjord, three prominent transverse ridges are 

also labeled as "moraines" (sheet 4). These bathymetric highs are inferred to be morainal banks 

composed primarily of coarse ice-contact material deposited during the retreat of Russell System. The 

mid-1870s and 1892 terminus positions correlate to the moraines south of Reid Inlet and at the mouths 

of Tarr and Johns Hopkins inlets, respectively. Within Johns Hopkins Inlet, a smaller, partially buried 

morainal bank, deposited around 1912, is still distinguishable across the inlet where it bends to the 

southwest. Seismic data reveal acoustic transparency at depth in some of these features, suggesting they 

are bedrock-cored and therefore sills, whereas others appear to be composed of purely discontinuous, 

hummocky, and mounded reflections interpreted to be ice-contact material (Cai, 1994). Consequently, 

the overall size of the feature is both a product of relict topography and the length of the interval of 

deposition. Extensive areas of the fjord walls are also characterized as moraine, which include remnants 

of kame terraces and partially buried terminal moraines. From an ecological perspective, these morainal 

forms can provide diverse habitats in relatively shallow water, as in Hugh Miller Inlet and near the 

mouth of Tidal Inlet. Deeper morainal deposits (below 80 m water depth) are typically buried under the 

hemipelagic drape that dominates the deeper basins.

The results of this study suggest that geoform, as inferred from bathymetric data, may not be an 

effective predictor of substrate in the active fjord environment. Consideration must also be paid to 

bathymetric position, water depth, and potential for sediment transport and removal, along with the 

influence of relict bathymetry. Within the West Arm, the only geoform that proved to be an accurate 

indicator of substrate was the fjord floor, which was 99 percent mud and most commonly associated 

with the mesobenthic depth zone (table 7, 8). This is not surprising, considering most of the hemipelagic 

sediment deposited within the fjord is eventually redistributed to the fjord floor basins, and few 
18

processes are capable of transporting abundant course material into the deep distal portions of the fjord. 

Substrate associations with other geoforms were more tenuous and are subject to the considerations 

enumerated above. Deltas, typically associated with sandy substrate, commonly have coarser topsets. 

Additionally the high influx of glacially sourced fines in the upper inlets can effectively bury active 

foresets in mud. Similarly, areas classified as wall are covered in a diversity of substrate types, but most 

commonly mud or unclassified unconsolidated sediment. Even steeply sloping bedrock outcrops were 

found to have significant mud cover. 

The geoform component is particularly useful in the West Arm for assessing areas of potential 

change. Large and rapid remobilization of sedimentary landforms has been observed in Glacier Bay 

(Hunter, 1994). Further, Glacier Bay is located in a seismically active region, because of its proximity to 

the Queen Charlotte-Fairweather Fault. In the event of a significant earthquake, the potential is high for 

catastrophic slope failures from fjord walls. Deltaic complexes are particularly susceptible to failure, 

because of their unconsolidated composition and position resting on very steep bedrock. Such a failure 

would result in widespread sediment redistribution into the deep basin areas, burying any marine life in 

its proximity. Activation of submarine landslides by wave activity is unlikely, however, as waves in the 

fjord are fetch-limited. There is also potential for landslide-induced wave activity, although the 

magnitude and severity of these events is unknown. 

Table 7. Percent mud cover versus geoform for the West Arm.

CMECS 

mesogeoform

Mud cover

Area (km2) Percent 

Moraine 89.5 79.6

Wall1 37.5 35.0

Floor 129.2 99.1

1 An additional 33.35 percent of wall forms are suspected of having unconsolidated sediment cover, most likely dominated by 

mud. 

Table 8. Major geoform distribution by depth zone for the West Arm.

CMECS 

Class

Shallow 

infralittoral:

Deep 

infralittoral: Circalittoral: Circalittoral 

(offshore): 

80–200 m water 

depth

Mesobenthic:

0–5 m water 

depth

5–30 m water 

depth

30–80 m water 

depth

200–1,000 m 

water depth

Percent Area 

(km2

) Percent Area 

(km2

) Percent Area 

(km2

) Percent Area 

(km2

) Percent Area 

(km2

)

Channel 0 0 0 0 0 0.77 2.9 1.02 3.9

Delta/fan 0.08 0.3 0.59 2.3 1.26 4.8 1.7 6.5 3.47 13.3

Floor 0 0 0.58 2.2 3.69 14.2 6.08 23.4 23.58 90.6

Moraine 0.16 0.6 3.27 12.6 4.35 16.7 8.77 33.7 13.3 51.1

Slump 0 0 0.04 0.1 0.05 0.2 0.14 0.5 0.04 0.2

Wall 0.19 0.7 4.04 15.5 6.81 26.2 7.92 30.4 8.69 33.4
19

Water Column Component

Water column interpretations in this study are derived from those presented in Trusel and others 

(2010) and Etherington and others (2007a). Similar to the benthic cover and geoform components, the 

water column component is classified within the estuarine system. Benthic depth zones associated with 

oceanographic stations in the West Arm are classified as circalittoral offshore (80–200 m) and 

mesobenthic (200–1,000 m). The upper water column within the West Arm (above the pycnocline) is 

always in the epipelagic water column depth zone (>0–200 m), while the lower water column varies 

between epipelagic and mesopelagic (200–1,000 m). 

Despite the fact that there is large spatial heterogeneity in tidal range within Glacier Bay (Hill, 

2007), all stations in Glacier Bay, including those in the West Arm, were classified by CMECS as 

moderate tide range (1–5 m). Similarly, although there is large spatial heterogeneity in tidal velocity 

throughout Glacier Bay, including regions of extreme tidal currents (Hill, 2007; Hill and others, 2009), 

the use of averages within the CMECS system defined energy intensity within the upper water column at 

all stations as low energy (very weak currents; 0–2 knots). For all stations in the West Arm except 

stations 6 and 7, the upper layer energy type is classified as current (due to freshwater discharge and 

down-Bay flow), while the bottom water column energy type is considered to be tide. Station 6 and 7 are 

more mixed and are influenced by tidal energy in both the upper and lower water layers. Energy 

direction in the upper water layers of the West Arm as well as the rest of Glacier Bay is considered 

horizontal.

Upper and lower water column temperatures in the West Arm were classified as cold (0–10°C). 

Across all the West Arm stations, bottom waters were classified as euhaline (30–40 psu). Upper water 

layers within the West Arm were mostly classified as mesohaline (5–18 psu), whereas the most seaward 

of the stations within the West Arm (station 6) was classified as polyhaline (18–30 psu). The averaging 

of salinity to obtain a single classification measurement removed the large seasonal variation in salinity 

patterns in the West Arm (see Etherington and others, 2007a). For all stations in the West Arm except 

station 6, the primary water source for the upper water layers is watershed due to the influence of 

freshwater discharge from glacier, snow, and groundwater sources, while the bottom layers are primarily 

influenced by local estuary exchange (tidal exchange that is primarily estuarine water). For station 6, the 

primary water source for both the upper and bottom water layers is local estuary exchange due to the 

more seaward location, shallower depth, and resultant higher mixing.

Macrohydroforms and mesohydroforms as defined by CMECS were not identified for Glacier 

Bay. The only identifiable CMECS lifeform was the phytoplankton maximum layer, which was assigned 

to the upper water layer for all oceanographic stations. Trophic status (defined as general categorization 

of the abundance of dissolved macronutrients (DIN and DIP) and level of primary productivity of a unit; 

Madden and others, 2008) is considered oligotrophic (<5 μg/L chlorophyll a) for both upper and lower 

water layers at all stations within Glacier Bay when averages are calculated over the whole year. No 

water column biotopes were identified.

Despite the highly variable nature of the water-column environment, particularly within an 

estuarine fjord system, the CMECS system provides only one opportunity to incorporate temporal 

variability (for all classes and attributes combined) into the classification of the water column. For all of 

Glacier Bay, the upper water column was classified with a temporal persistence value of variable (varies 

regularly), while the persistence of the bottom water layers was considered permanent (stable). It was 

not possible to identify multiple sources of variation (for example, seasonal plus stochastic), so the 

dominant source of temporal change (seasonal) was defined.

Using the CMECS classification system, the water column properties that illustrated the greatest 

amount of spatial variation in Glacier Bay, horizontally (among stations) and (or) vertically (between the 

upper and lower water layers), include benthic depth, salinity, energy source, and primary water source 
20

(fig. 7). Upper water layers demonstrate greater complexity than the bottom water layers, with a greater 

number of unique combinations of classes (habitat units) in the upper layer. There were only two bottom 

water layer habitat units in the West Arm that vary only in benthic depth zone, with station 21 exhibiting 

shallower depth than the rest of the West Arm (fig. 7A). Within the West Arm, there were four different 

habitat units of the upper water layer that varied by benthic depth, salinity, energy type, and primary 

water source (fig. 7B). The majority of the upper water column within the West Arm is composed of 

mesohaline waters that are mainly influenced by watershed sources and current energy within 

mesobenthic depths. Upper water layers of station 21 differ from the mainstem waters of the West Arm 

only in the benthic depth zone (circalittoral offshore). The upper water column habitats of station 6 

differ from the other West Arm stations more substantially, with different classes of salinity, energy 

type, and primary water source that reflect its more seaward location. 

Sediment Accumulation

Average annual sediment accumulation rates for the period 1970 or 1972 to 2009 are shown in 8. 

Some basin-floor areas within the West Arm have no accumulation or even slight erosion (fig. 8: ~ 0 

m/yr). Lacking evidence of strong currents, such areas are thought to be beyond the resolution of our 

data and are inferred to receive a low debris flux similar to the surrounding benthic environment. 

Figure 7. Maps of (A) upper and (B) bottom water column CMECS habitats in Glacier Bay areas (Trusel and 

others, 2010)
21

The West Arm can be divided into two modern sedimentation regimes: glacial sedimentation in the 

upper ice-contact basins of Tarr and Johns Hopkins Inlets and a marine paraglacial sedimentation regime 

that exists in all basins in the lower West Arm. Measured rates in the upper basins average 0.6 m/yr, 

whereas in the lower basins sediment accumulation rates are far less, averaging 0.1 m/yr. If the influence

Figure 8. Map of average annual sediment accumulation rates for 1970 and 1972 to 2009.
22

of Queen Inlet is excluded, average sedimentation rates for the lower West Arm approach 0 m/yr yet are 

still sufficient to drape the seascape in glacimarine mud. The West Arm can be split into two primary 

physical benthic environments. The upper West Arm receives significant sediment flux, increasing the 

likelihood of gravity flows along the steep fjord walls, morainal banks, and ice-contact deltas. 

Terrestrially-sourced rock falls and debris flows are also more prevalent, owing to the steep relief of the 

fjord walls and limited vegetation cover associated with recent glacial retreat. Conversely, the lower 

West Arm is characterized by a more static benthic environment with a lower potential for 

unconsolidated slope failures. Notable exceptions to this general rule are found in Queen and Tidal 

Inlets. Fed by nearby Carroll Glacier, the relatively high sediment flux into Queen Inlet is anomalous 

within the lower West Arm, creating a physical benthic environment that is inferred to be intermediate 

to those that typify the upper and lower West Arms. Sedimentation rates in the vicinity of Queen Inlet 

average 0.4 m/yr, with the bulk sediment accumulating near the fjord-head delta and the submarine fan 

at the mouth of the inlet. Due to data quality issues in the historical bathymetry, Tidal Inlet was excluded 

from the differential bathymetric analysis presented in this study. However, numerous slide and slumplike features are evident in the modern bathymetry (sheet 3: slump mesogeoform), suggesting that the 

benthic environment within Tidal Inlet is relatively dynamic compared to the mainstem of the West 

Arm. While the frequency of such events is unknown, they potentially pose a significant disturbance to 

the benthic communities along the fjord wall.

Sediment accumulation decay downfjord is not only a function of distance from the glacial 

termini but is also influenced by submarine landforms. Sedimentation decreases abruptly south of the 

morainal bank at the mouth of Tarr Inlet (sheet 4: moraine mesogeoform). Historically, this bank has 

acted as a dam to the downfjord transport of sediment via bottom currents, confining the majority of 

sediment originating from Margerie and Grand Pacific Glaciers within Tarr Inlet (Cai, 1994). However, 

the 2009 bathymetry indicates the morainal bank may have reached its capacity as a sediment trap. If 

this is the case, sediment may begin to bypass Tarr basin, forming a fan at the mouth of the inlet. There 

are already signs of slope failure and possibly incision along the West end of the fjord-mouth morainal 

bank, evident in the 2009 bathymetry. This knickpoint may eventually propagate upfjord, creating a 

direct pathway for sediment transport into the mainstem of the West Arm. Eventually the spatial pattern 

of sedimentation in Tarr Inlet may take a form similar to that observed in Queen Inlet, with two main 

loci of deposition: one at the fjord head and another at a fjord mouth fan. Whether or not this occurs and 

to what extent depends on the composition of the morainal bank. Seismic reflection profiles indicate the 

bank may be primarily bedrock cored with a thin veneer of unconsolidated sediment (Cai, 1994), 

restricting submarine incision. If, however, the sill only extends across a portion of the fjord mouth, as 

in neighboring Johns Hopkins Inlet, incision and slope failures could potentially excavate the 

unconsolidated portion of the morainal bank. The most recent bathymetry does not provide a conclusive 

answer, but it tends to support the latter scenario (fig. 9).

Sediment accumulation occurring in the most proximal basin has ramifications for local benthic 

life, because of the pronounced sediment flux but also for glacier dynamics. Grounding-line deposits act 

as a second-order control on the stability of glacier termini (Powell, 1991; Fischer and Powell, 1998), 

and the development of an efficient pathway for sediment transport away from the grounding line could 

reduce terminus stability.

Benthic Habitats

Previous research has demonstrated classes of three bottom types most important to benthic

organisms: soft-flat bottom, mixed bottom including coarse sediment and low-relief rock with low to 

moderate rugosity, and rugose-hard bottom (Greene and others, 2007; Cochrane, 2008). The West Arm 

has all of these of habitats, with the greatest abundance being soft-flat bottom. In Glacier Bay, species 
23

Figure 9. Perspective view and cross section of the morainal bank at the mouth of Tarr Inlet.

associated with soft-flat bottom habitats include gastropods, algae, flatfish, Tanner crabs, shrimp, sea 

pen, and other crustaceans (Etherington and others, 2007b). In the bay proper, soft corals and sponge are 

the only species found associated with boulder substrate (Etherington and others, 2007b). Our video 

observations suggest that geological-biological associations found in central Glacier Bay to be at least 

partially analogous to associations in the West Arm. Given that soft mud substrate is the most prevalent 

habitat in the West Arm, it is expected that the species associated with a soft bottom in the bay proper 

are the most abundant types of species within the West Arm. While mud is the dominant substrate 

throughout the fjord, the upper and lower West Arm are potentially very different environments owing 

to the spatially and temporally heterogeneous influence of glaciation and associated effects on fjord 

hydrologic and oceanographic conditions. Therefore, we expect variations in the distribution of species 

accordingly.

The distribution of Tanner crab (Chionoecetes bairdi), a mud-associated species, may be a 

potential example of the two contrasting environments. Systematic sampling shows that Tanner crabs 

are found throughout the West Arm but are generally most abundant near fjord-mouth sills and sparse in 

the ice-contact inlets and the deeper fjord basins (Mondragon and others, 2007a; Nielsen and others, 

2007). Juvenile females were very dense in Scidmore-Charpentier Inlet, which is hypothesized to 

represent a suitable habitat for juveniles as opposed to adults, because of the generally lower biomass 

and food resources associated with glacial proximity (Nielsen and others, 2007). Relative to the upper 

West Arm, however, Scidmore-Charpentier receives a much lower glacial debris flux. Indeed, the upper 
24

West Arm is likely a much harsher environment because of the extreme glacial influence and associated 

characteristics. The higher sediment flux may explain why juvenile Tanner crabs were not abundant in 

the similar soft bottom habitat near the upper West Arm glaciers.

The West Arm has both shallow- and deep-water benthic habitats. However, unlike Glacier Bay 

proper where large contrasts in the depth and current velocity define habitats (Etherington and others, 

2007b), current velocities are relatively low for most of the West Arm (Etherington and others, 2007a; 

Hill, 2007). Therefore, while substrate and current exposure are the dominant factors controlling species 

distribution in the Bay proper (Etherington and others, 2007b), currents are not as likely to play as large 

of a role in the West Arm. We expect substrate type and glacial proximity to be the most important 

habitat variables in the West Arm, although further groundtruthing is necessary to fully evaluate this 

hypothesis.

Conclusions

Seafloor substrates and morphology in the West Arm were mapped using a combination of data 

sources including multibeam bathymetry, video observations, backscatter data, and knowledge of the 

glacimarine environment. Substrate characterization, combined with information about depth, 

morphology, glacial influence, and current velocity provide the necessary variables to define potential 

benthic habitats in the West Arm. Mud is the dominant substrate within the West Arm, covering nearly 

72 percent of the seafloor. Bedrock was the next most abundant substrate, covering about 7 percent of 

the surveyed area. The remaining portion of the West Arm is covered by a mixture of coarser sediment 

and boulder/rubble. We expect organisms found associated with similar habitats in the bay proper are 

also abundant in the West Arm, with the largest benthic communities being those associated with mud 

substrate.

The bulk of sediment flux from Johns Hopkins, Margerie, and Grand Pacific Glaciers is confined 

to the Upper West Arm basins. Because of the contrast in sediment accumulation rates between the 

upper and lower West Arm, the fjord can be characterized as two distinct regions—the dynamic Upper 

West Arm characterized by an extremely high glacial sediment flux and the relatively static Lower West 

Arm. The exceptions are the vicinity of Queen Inlet, which receives abundant sediment from Carroll 

Glacier, and Tidal Inlet, which is prone to mass wasting due to its steep, poorly consolidated valley 

walls. The benthic environments typical of the Lower West Arm can be further subdivided into the 

mesobenthic basin constrained to the West Arm proper and the predominately circalittoral bays and 

inlets.

Glacial meltwater and debris flux are known to affect the spatial distribution and variety of 

benthic fauna and flora in the arctic (for example, Wlodarska-Kowalczuk and Pearson, 2004) and to 

control the distribution and diversity of wall communities in Tarr Inlet, in spite of adequate nutrient 

supply (Carney and others, 1999). However, the degree to which these variables act as physical controls 

in the deep basins is unknown. The temperate glacimarine environment, with some of the highest 

sediment fluxes recorded worldwide, may limit the diversity, abundance, and distribution of these 

benthic communities, particularly in upper Tarr and Johns Hopkins Inlets where sediment flux is 

pronounced. Likewise, there exists the potential for areas of intermediate disturbance along the fjord 

axis that likely support higher diversity and abundance. Further study of the seafloor environment in the 

upper fjords is critical for a more quantitative evaluation of these relations. However, the extreme 

turbidity of the water column in the ice-proximal portions of these basins may limit the effectiveness of 

video observation.
25

Management Implications

This work presents the first surficial geology and geoform maps for the West Arm of Glacier 

Bay. Substrate, morphology, depth, water column, and glacial processes are all important factors in 

determining the distribution, abundance, and diversity of demersal and benthic marine life. Therefore, 

these products are important to scientists and managers to better understand the capacity of the West 

Arm to act as a marine reserve. These results are a baseline for the assessment of future environmental 

change, resulting from the influences of proximal glaciation, as well as dynamic fjord processes. With 

stresses on the glacial estuary because of amplified high-latitude climate change and the commercial, 

recreational, and scientific importance of the Glacier Bay ecosystem, a full understanding of the modern 

system is fundamental for understanding its resources and developing the most appropriate management 

strategies.

Acknowledgments

Funding for this benthic habitat study was provided by the National Park Service. The authors 

would like to thank Luke Trusel for providing the boilerplate of his habitat study in Muir Inlet. Special 

thanks to the captain and crew of R/V Steller, as well as Gerry Hatcher and Jamie Grover of USGS for 

their efforts in our field operations. Assistance from Nadine Golden with USGS mapping standards is 

greatly appreciated. 

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