BULLETIN OF MARINE SCIENCE, 69(2): 685699, 2001

EFFECTS OF THE WATER COLUMN ON HYPERSPECTRAL

REFLECTANCE OF SUBMERGED CORAL REEF FEATURES

Heather Holden and Ellsworth LeDrew

ABSTRACT
Remote sensing technology has many attributes that would be beneficial to monitoring
submerged coral reef ecosystems, such as the ability to revisit a large study area repeti-
tively and consistently without the necessity of large teams of field researchers. One
limiting factor, however, is the difficulty in accounting for the variable effects of the
water column on the optical reflectance characteristics of submerged features. These vari-
able water column effects have been observed as depth, bottom-type, and wavelength
dependent; such complex modifications limit the accuracy of remote identification of
submerged coral reef features. In a preliminary attempt to examine the extent of the
problem in a complex coral reef ecosystem, in situ hyperspectral reflectance measure-
ments were collected in the U.S. Virgin Islands at various depths over different substrate
types in water of consistent optical quality. A comparison is made between hyperspectral
reflectance measured at the top and bottom of the water column in different water depths
over different substrate types in an effort to alert users of remotely sensed data of the
potential problems of identifying submerged features without appropriate corrections.
While most coral reef remote sensing projects assume vertical and horizontal homogene-
ity of water optical properties and consider variation in optical reflectance representative
of change in bottom type, this preliminary study reveals that the case is more complex
and appreciable effort must be made to correct for the effects of the water column for
accurate identification of submerged features.

One of the most important limitations in assessing the effects of stress on coral reefs is
the general lack of quantitative data, both spatial and temporal (Grigg and Dollar, 1990).
Although remote sensing technologies have great potential in overcoming this quantita-
tive void, there are many complications associated with extracting valuable information
from imagery with confidence. The utility of remote sensing has been investigated to
determine its ability to gain information on the geographic extent of various benthic habi-
tats and substrate types (e.g., Lyzenga 1978, 1981; Bina et al., 1979; Jupp et al., 1985;
Bour et al., 1986; Ackleson and Klemas, 1987; Bour, 1988; De Vel and Bour, 1990;
Loubersac et al., 1991; Hardy et al., 1992; Zainal et al., 1993; Michalek et al., 1993;
Luczkovich et al., 1993; Bierwirth et al., 1993; Morel, 1996; Clark et al., 1997; Mumby et
al., 1998; Myers et al., 1999).
In most cases, to account for the effects of water depth and turbidity variation, remotely
sensed images have been assumed horizontally and vertically homogeneous, and correc-
tions have been applied to the entire image by subtracting a constant digital value or
computing ratio values (e.g., Lyzenga, 1978; Bour et al., 1986; Estep, 1991). The as-
sumption of homogeneity within the vertical water column and the horizontal water sur-
face is, however, unrealistic in many coastal coral reef environments. A review of the
majority of these studies can be found in Holden and LeDrew (1998a).
Remote sensing is an excellent option for consistent, repetitive monitoring of submerged
coral reef and related ecosystems, especially for large or remote areas; however, there are
two major technical issues that must be resolved before accurate assessment of submerged
ecosystems can be accomplished using passive remote sensing technology. The first prob-

685
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lem is that several common coral reef features have optically similar characteristics such
that it is difficult to discriminate between algae-covered dead coral, seagrass, and healthy
coral. Therefore, if visual analysis is performed on remotely sensed imagery, there will be
significant confusion and resultant misclassification. If high spectral resolution
(hyperspectral) passive reflectance (using only reflected solar energy) is considered, there
are subtle differences at specific wavelengths between optically similar features that al-
low discrimination. Previously, using a large hyperspectral library or database, we have
shown that there are differences in hyperspectral in situ reflectance characteristics be-
tween common coral reef features (Holden and LeDrew, 1998b,1999, 2000).
The second major problem involved with remote sensing of submerged ecosystems is
that the water column affects the signal received at the sensor, depending on the water
depth, water quality, and subsurface brightness. There has been increased confidence in,
and use of, hyperspectral remote sensing technology as a mapping and monitoring tool
for coastal environments, but insufficient attention among the remote sensing community
has been given to the complex and variable problems involved with accounting for effects
of the water column.
Radiative transfer algorithm development is currently being undertaken by a small num-
ber of researchers to characterize the behavior of radiation when influenced by the highly
attenuating water column and a highly reflective bottom. Radiative transfer theory pro-
vides a connection between inherent and apparent optical properties where inherent opti-
cal properties depend only upon the medium and are therefore independent of the ambi-
ent light field, while apparent optical properties depend on both the medium and the
geometric structure of the ambient light field (Mobley, 1994).
A commonly used apparent optical property is the spectral irradiance reflectance fac-
tor, R (z, l), (hereafter referred to as reflectance) defined as the ratio of spectral up-
welling, Eu (z, l), to downwelling, Ed (z, l), irradiance. This value was measured at the
bottom of the water column, just above the substrate, and at the top of the water column,
just below the water surface. The reflectance just below the water surface is used to avoid
including the effects of the water surface in the comparison between top and bottom of
the water column reflectance. The measurements used here allow for an investigation of
the effects of the water column on hyperspectral reflectance when considering different
depths and bottom types. This preliminary case study was designed to examine the in situ
hyperspectral reflectance characteristics of submerged coral reef features at various depths,
and the change in hyperspectral reflectance between the surface and the bottom of the
water column.
Previous work has focused on creating a spectral library of reflectance characteristics
of common coral reef features (Holden and LeDrew, 1998b, 1999) without considering
the effects of the water column. The spectral library has been based on measurements
taken at the bottom of the water column in order to determine the spectral reflectance
characteristics of the features alone without the interference of the water column. We
believe this approach to be the most robust means of determining the pure or endmember
reflectance characteristics of submerged features since the effects of the water column
will vary with water depth and quality.
This, however, is not the spectral reflectance that a remote sensor would detect because
the water column overlying the submerged features alters the reflectance response through
absorption and scatter. The degree to which absorption and scatter occurs is a function of
water depth, water quality, and substrate brightness, but certain generalizations may be
 HOLDEN AND LEDREW: HYPERSPECTRAL REFLECTANCE OF SUBMERGED CORAL REEF FEATURES 687

possible. The sampling strategy in this initial study was not to measure a large number of
endmember, or pure, spectra, but rather to measure the reflectance just above common
substrates as well as at the top of the water column, yet still above that same substrate. The
goal of this study is to examine and describe the change in hyperspectral reflectance of
submerged coral reef features with the addition of the overlying water column. While we
have previously shown that there are subtle differences between optically similar coral
reef features within narrow wavelength regions, we have not shown that these differences
are still detectable once the water column is an additional variable to be considered.

BACKGROUND

INHERENT OPTICAL PROPERTIES.If a wavelength-specific collimated beam of light illu-

minates a volume of water, a fraction of the energy will be absorbed within the volume of
water, a fraction will be scattered out of the beam in all directions, and a fraction will be
transmitted through the volume with no change in direction. The inherent optical proper-
ties usually used in hydrologic optics are the spectral absorption and scattering coeffi-
cients. Inherent optical properties can be measured using small samples of water, and
they are independent of the environment from which the sample was taken, however, it is
generally quite difficult to measure inherent optical properties in situ. The beam attenua-
tion coefficient is the only inherent optical property routinely and accurately measured in
situ (Mobley, 1994).
The majority of energy entering the water column is absorbed (Kirk, 1983). Absorption
itself is a fundamental process that determines the shape and magnitude of the reflectance
spectrum in the water, while an absorption coefficient accounts for the proportion of light
lost due to this absorption (Pegau, 1995). The absorption coefficient is an important pa-
rameter that describes the influence of dissolved and suspended matter on the propaga-
tion of energy in the water column (Prieur and Sathyendranath, 1981).
The variation in spectral absorption coefficients of all light absorbed in natural water is
attributed to three components: (1) the water itself, (2) yellow substance, or dissolved
organic matter (DOM), and (3) phytoplankton (Prieur and Sathyendranath, 1981). The
first component, water, has weak absorption in the blue and green portions of the electro-
magnetic spectrum, but increases significantly for wavelengths greater than 550 nm (Kirk,
1983). Secondly, yellow substance, or DOM (dissolved organic matter), resulting from
decomposition presents significant consequences for light absorption in the blue end of
the spectrum. Finally, phytoplankton absorbs strongly in the red region depending on the
total amount of photosynthetic pigments.
While most light in the water column is absorbed immediately, many photons are sin-
gly or multiply scattered before being absorbed. Since scatter does not remove light, but
simply diverges light from its original path, it effectively impedes the vertical penetration
of light. The result is that photons bounce off particles, which increases the total path
length thus increasing the probability of being absorbed (Kirk, 1983). Unfortunately, there
is no direct measure of scatter, but since turbidity is directly related to scatter, a nephelo-
metric turbidimeter can be used as an indirect measure of scatter within the water col-
umn.
The preceding discussion has assumed no inelastic scattering processes, whereby a
change in wavelength occurs. Inelastic scattering does occur in natural waters due to
688 BULLETIN OF MARINE SCIENCE, VOL. 69, NO. 2, 2001

fluorescence of chlorophyll in phytoplankton at about 685 nm, or Raman scattering by the

water molecules themselves between 550 and 650 nm (Mobley, 1994). The processes of
both fluorescence and Raman scatter serve as internal sources of energy, as light is scat-
tered inelastically from shorter to longer wavelengths. With an internal source of light, it
will appear that less energy is being absorbed at that wavelength resulting in inaccurate
coefficient measures.
The beam attenuation coefficient is defined as the fraction of incident light absorbed
and scattered within a layer of given thickness (Kirk, 1983). Beam attenuation results
from the combined action of scattering and absorption, but is primarily an absorption
effect in the visible region. The value of the beam attenuation coefficient can be obtained
by measuring the extinction in intensity of a beam of light passing through a medium, but
it is difficult to establish the relative contribution of scattering and absorption to the total
beam attenuation (Kirk, 1983). All of the radiative loss processes can be accounted for in
the single measurement of beam attenuation at the wavelength of interest (Mobley, 1994).
APPARENT OPTICAL PROPERTIES.When radiometric characteristics are used to describe
the light field in a water body, the properties are referred to as apparent and are only
indirect measures of the water column. An ideal apparent optical property changes only
slightly with external environmental variation, but changes enough from one body to the
next to allow characterization (Mobley, 1994). One such apparent optical property is the
diffuse attenuation coefficient (K). There is a diffuse attenuation coefficient for any radio-
metric variable, but the most commonly used is the spectral diffuse attenuation coeffi-
cient for downwelling irradiance. Under typical oceanic conditions, irradiance (Ed) de-
creases approximately exponentially with depth; this exponential decay is characterized
by the diffuse attenuation coefficient, which can be determined from the measurement of
the rate of change (slope) of the log of downwelling irradiance vs. depth profile, or de-
fined as:

Kd (z,l) = [1/Ed (z,l)] * [d Ed (z,l) / d z]

The distinction between beam, c (l), and diffuse, Kd (z,l), attenuation coefficients is
important: c (l) is defined in terms of the radiant power lost from a single, narrow, colli-
mated beam of photons, while Kd (z,l) is defined in terms of the decrease with depth of
all photons heading in a downward direction (Mobley, 1994). Kd (z,l) depends on the
directional structure of downwelling irradiance, so it is classified as an apparent optical
property.
LITERATURE REVIEW.Lyzenga (1981) attempted to extract bottom-type information
from Landsat MSS data with an algorithm based on the assumption that the bottom-
reflected radiance is approximately a linear function of the bottom reflectance and an
exponential function of water depth. The first step in this technique was to transform the
digital number (DN) radiance according to:

Xi = ln (Li Lsi)

where, Li is the DN in band i and Lsi is the deep-water radiance, so if Xi is plotted vs Xj

over a uniform substrate, the data points will fall along a straight line with a slope of Ki/
Kj, where Ki is the attenuation coefficient in that band. Data from a different bottom type
will theoretically fall along a parallel line with a displacement equal to the change in
 HOLDEN AND LEDREW: HYPERSPECTRAL REFLECTANCE OF SUBMERGED CORAL REEF FEATURES 689

bottom reflectance between the two bottom types. This transformation technique relies on
the assumption that Lsi is completely unaffected by bottom reflectance, so subtracting this
value from the signal over a particular bottom type will remove the effects of the water
column. However, the selection of Lsi may be an arbitrary decision based on knowledge of
the area of interest, and there can be no guarantee that the pixel is not influenced by
bottom reflectivity. The result of this transformation, therefore, may still confuse varia-
tion in bottom type with variation in depth. Additionally, the transformation results in a
significant loss of spectral information, which would confound substrate identification.
Jupp et al. (1985) defined a set of algorithms for mapping water depth and substrate
types on the sea floor that have been incorporated into the BRIAN (Barrier Reef Image
Analysis) system developed to aid planning and management of the Great Barrier Reef
region using Landsat data. According to Jupp (1985), the interpretation of the depth zones
depends on the spatial homogeneity of the water mass and the substrate below (which is
not normally an assumption that can be made), and further algorithm improvement is
required for successful use in detailed mapping of submerged habitats.
Philpot (1987) described the ocean color of optically shallow stratified waters using a
singly scattered irradiance (SSI) model as an approximate radiative transfer equation,
although multiple scattering is included implicitly. Conceptually, downwelling light at
the water surface is attenuated by backscattering and absorption as it travels downwards
to a depth at which the single scattering event occurs. After this single scattering event
occurs, the scattered light is traced back upwards to the water surface, attenuated only by
absorption and not scattering. A single-scattering coefficient, Bss, is defined for a water
layer of thickness dz as:

Bss (z) = dEu (z)/[Ed (z) dz]

Philpots (1987) model is capable of an accurate qualitative description of the varia-

tions in reflectance recognizing that vertical inhomogeneities in the optical properties of
the water column could significantly affect remote observations of water color.
Estep (1991) developed a model to quantify the contamination of the downwelling
light stream by bottom-reflected light by treating the bottom sediments as the source of
light. The model is an inversion of the single scatter irradiance (SSI) model constructed
by Philpot (1987), which assumes optically shallow, stratified waters. Esteps model, used
with several field data sets, revealed that the contamination in the downwelling spectrum
depends on wavelength and increases with closer proximity to the bottom. Estep (1991)
also concluded that a decrease in water clarity (or an increase in water attenuation) results
in diminished contamination of the upwelling light stream, and that increased bottom
reflectance increases the contamination seen in the downwelling light stream.
Bierwirth et al. (1993) attempted to separate the depth variation effect from an image
by considering substrate reflectance and depth in the same algorithm. A water reflectance
model was used to estimate both water depth and substrate reflectance at each pixel based
on:

ln (Ri) = ln (Rbi) 2KiZ

The corrected Landsat TM pixel value is Ri, the substrate reflectance is Rbi, the attenu-
ation coefficient is Ki, and the depth is Z. Requirements for the model were raw TM
690 BULLETIN OF MARINE SCIENCE, VOL. 69, NO. 2, 2001

multitemporal data, derived attenuation coefficients, and derived bathymetric data. At-
tenuation coefficients were determined by selecting areas on the TM image with the same
substrate, but differing water depths.
This method unmixes the exponential influence of depth in each pixel through the use
of a mathematical constraint, which leaves a multispectral residual representative of rela-
tive substrate reflectance. Such an attempt is valid for multispectral imagery, however
difficulties arise when attempting to identify substrate types based on established library
endmember spectra due to the transformation of reflectance. Furthermore, deriving at-
tenuation coefficients from Landsat TM imagery (with 30 30 m pixels) requires inti-
mate knowledge of the study site, since the operator needs to identify pixels with homo-
geneous bottom types, yet be certain of variable water depths.
Maritorena (1996) proposed a means of assessing the diffuse attenuation coefficient
from remotely sensed data by linearizing the raw data according to Lyzengas (1978,
1981) method, identifying pixels with homogeneous bottoms at various depths on a satel-
lite image, and estimating attenuation from pairs of pixels. Using in situ measurements,
Maritorena (1996) determined downwelling irradiances (Ed) at two different depths (Z1,
Z2) to obtain wavelength (l)-dependent attenuation coefficients (Kd) according to:

Kd (l)(Z1, Z2) = (Z1, Z2)-1 ln [Ed (l)(Z1)/Ed (l)(Z2)]

The ratio of attenuation coefficients was calculated for SPOT XS1 and XS2, and the
axes rotated to reveal an image free of water column effects, which is considered repre-
sentative of bottom type only. The resulting image has only one channel where radiance
varies from white to black with decreasing reflectance of bottom features from bright
sand to dark vegetation, for example. The interpretation of this monochannel image is
limited by the lack of multispectral information. This procedure demands accurate knowl-
edge of water depth and bottom type before selection of pixels, which are not often known
in shallow coral reef environments. It would also be very difficult to select a variety of
pixels with confidence that the bottom is homogeneous.

DATA COLLECTION

Data collection took place during February 1999 within Buck Island National Monu-
ment, St. Croix, U.S. Virgin Islands in the Caribbean (Fig. 1). The objective was to mea-
sure and describe the effect of the water column on the hyperspectral reflectance charac-
teristics of submerged features. The motivation behind this initial project was to deter-
mine if the subtle spectral reflectance differences identified without the influence of the
water column are still present once a water layer of variable thickness is added to the
equation.
To meet this objective, hyperspectral reflectance spectra were measured at the bottom
of the water column just above the substrate as well as at the top of the water column just
below the surface. The measurements taken at the top of the water column are, theoreti-
cally, the composite of the reflectance spectra of the substrate alone plus the effects of the
water column between the bottom and the sensor. Measurements were taken in a variety
of water depths ranging from 1.5 to 11.7 m in the forereef and backreef environments, as
well as in a seagrass lagoon. The field season was short (only 8 d on the water in total, due
 HOLDEN AND LEDREW: HYPERSPECTRAL REFLECTANCE OF SUBMERGED CORAL REEF FEATURES 691

Figure 1. Data collection took place in the coral reefs surrounding Buck Island, St. Croix, U.S.
Virgin Islands.

in part to poor weather conditions), so the data set consists of 17 pairs of spectra. We
acknowledge that this is a relatively small number of spectra, but suggest that it is suffi-
cient as a preliminary study leading to future field data collection.
The reflectance measurements at the top and bottom of the water column were taken
with a hyperspectral radiometer (Analytical Spectral Devices Personal Spectrometer II).
While the radiometer itself remained on board the boat with an operator who controlled
the integration time, a 20 m underwater optical cable allowed a SCUBA diver to carry the
actual sensor underwater for the measurements. The underwater sensor used had a field of
view (FOV) of 22. The determination of reflectance requires two separate and sequential
measurements with the 22 FOV sensor. First, the total incoming radiance is measured
using an underwater reference panel by holding the sensor at nadir just above the panel.
This acts as a reference or normalizing measurement. Immediately following each of
these reference measurements, upwelling radiance is measured by holding the sensor at
nadir 10 cm below the water surface, or 10 cm above the bottom, as the case may be. The
ratio of upwelling radiance to downwelling radiance provides a measure of the reflec-
tance factor, referred to conventionally as simply reflectance.
The area on the bottom that is in the field of view of the sensor will be different depend-
ing on the height above the bottom. When the sensor is held 10 cm above the substrate at
the bottom of the water column, the radius of measurement will be 1.94 cm according to:

Radius = d * tan (FOV/2)

where d is the distance or height above the bottom and FOV is the field of view of the
sensor (22). When the top of the water column measurement is made, the radius of the
circle measured will differ depending on the water depth. The deepest profile was mea-
sured in 11.7 m water depth, so the radius of the area of the substrate measured at the top
of the water column is 2.27 m. The shallowest profile was measured in 1.5 m water depth,
so the radius of the measurement area is 29.16 cm.
The area of measurement is therefore different at the top of the water column than at
the bottom, so study sites were chosen based on homogeneous bottom types such that the
substrate reflectance could not change appreciably with a change in area measured. A
photographic record of the substrate type was taken at the time of measurement, and
support staff at Buck Island National Park identified coral samples.
692 BULLETIN OF MARINE SCIENCE, VOL. 69, NO. 2, 2001

Figure 2. Five separate spectral pairs were measured in the forereef environment in depths ranging
from 5.4 to 11.7 m.

DESCRIPTION OF SPECTRAL PAIRS

The spectral pairs were divided into categories based on environment (forereef and
backreef) and bottom type for ease of comparison. Five categories were defined: forereef
(5 pairs), coral and sand in the backreef (5 pairs), bleached coral in the backreef (3 pairs),
sand/rock and algal growth in the backreef (3 pairs), and seagrass (1 pair). The change in
spectral reflectance between the bottom and the top of the water column was found by
subtracting the surface spectra from its corresponding bottom spectra. The resulting dif-
ference spectra reveal the magnitude and shape of the changes occurring within the wa-
ter column.
FOREREEF ENVIRONMENT.The spectral pairs measured in the forereef environment are
compared in Figure 2. The spectral reflectance measured 10 cm below the water surface is
lower at all wavelengths than the reflectance measured 10 cm above the substrate. The top
of the water column measurements are lower in spectral reflectance because the light
must pass down and back up through the water column (2-stream) with attenuation along
 HOLDEN AND LEDREW: HYPERSPECTRAL REFLECTANCE OF SUBMERGED CORAL REEF FEATURES 693

Figure 3. Coral and sand substrates found in a patch reef environment in the backreef are compared.

both paths before being measured by the sensor. Conversely, the bottom of the water
column measurements are higher in spectral reflectance magnitude because the light need
only pass down the water column (1-stream) before being measured by the sensor. There
is a slight dip in spectral reflectance at 515 nm observable in the surface measurements in
all cases. This spectral dip is only observable in the bottom measurement taken in 11.7 m
water depth.
In the case of the two deepest profiles (11.7 and 7.8 m), the reflectance drops to zero
beyond approximately 600 nm for both the top and bottom of the water column measure-
ments, indicating that the deep water absorbs all of the reflected energy in this wavelength
region. Interestingly, the measurements made in 7.5 m water depth reveal that energy is
absorbed above 600 nm only when the measurement is taken at the top of the water col-
umn, but there is detectable reflection at the bottom of the water column above 600 nm.
This observation is different than the profile measured in 7.8 m, although the difference
in depth is small (0.3 m). One explanation for the different observations at similar water
depths is the different substrate brightness: dead coral and algae at 7.8 m and dead coral
694 BULLETIN OF MARINE SCIENCE, VOL. 69, NO. 2, 2001

Figure 4. Spectral pairs measured over sand and rock with algal turf in the backreef environment.

and sand at 7.5 m. The profiles measured in both 6 m (sand) and 5.4 m (coral) reveal that
the reflected light above 600 nm drops to a very low magnitude for the surface measure-
ments.
CORAL AND SAND IN THE BACKREEF ENVIRONMENT.The next group of spectral pairs or
profiles considered was measured over a coral and sand substrate in a patch reef environ-
ment in water depths ranging from 4.6 to 1.5 m. As in the forereef environment described
above, there is a spectral reflectance dip at 515 nm apparent in the measurements taken at
the surface, but not in the measurements taken at the bottom. The four deepest profiles
(4.6, 3.5, 2, and 1.8 m) exhibit different relationships between top and bottom of the water
column reflectance than those observed in the forereef environment above. In these four
cases, the measurements taken at the surface have greater magnitudes of reflectance than
the measurements taken at the bottom of the water column in the shorter wavelengths, but
this relationship reverses in the longer wavelengths. The wavelength at which this rever-
sal takes place is different for all four cases (515, 580, 555, and 507 nm, in order of
decreasing depth). The profile measured in 1.5 m water depth reveals the same relation-
ships observed in the forereef environment: surface measurements exceed bottom mea-
surements at all wavelengths.
The combination of bright substrate (50% sand cover) and shallow water may contrib-
ute to the explanation of the observation that surface reflectance is higher than bottom
reflectance in the shorter wavelengths. Light energy must travel down the water column
before interacting with the bottom and traveling back up the water column to be captured
by the sensor. It is therefore expected that the magnitude of reflectance would be lower at
the top of the water column than at the bottom, as is the case in the longer wavelengths.
The observation that in four of the five cases the light energy available is actually greater
at the top of the water column than the bottom is confounding and suggests that the
commonly assumed exponential decrease of energy with depth is not necessarily the case.
 HOLDEN AND LEDREW: HYPERSPECTRAL REFLECTANCE OF SUBMERGED CORAL REEF FEATURES 695

Figure 5. Seagrass was measured in a water depth of 5.4 m.

SAND AND ROCK WITH ALGAL GROWTH IN THE BACKREEF ENVIRONMENT.Sand and rock
with algal turf are the profiles considered in Figure 4. There are three profiles over similar
substrates in water depths ranging from 3.9 to 4.0 m. As with the coral and sand profiles
above, the surface reflectance measurements are actually higher than the bottom mea-
surements in the shorter wavelengths while the bottom measurements are greater in mag-
nitude than those at the surface in the longer wavelengths. Also, as with the coral and sand
profiles above, the wavelength at which this reversal occurs is variable: 578, 571, and 557
nm in order of decreasing depth. In all three cases below, there is a dip in spectral reflec-
tance at 515.6 nm at the surface, which is not observable at the bottom of the water
column, suggesting that this spectral feature is a function of the water itself and not the
substrate.
SEAGRASS LAGOON.One profile was measured in a seagrass lagoon environment with
a water depth of 5.4 m. Like the forereef environment, the measurements taken at the
surface display greater magnitude of reflectance than the measurements taken at the bot-
tom of the water column. Also, the spectral reflectance dip at 515 nm is present in the
surface measurements; however, it is also present in the bottom measurements. The sub-
stance in the water column responsible for this spectral dip may also be present in the
seagrass substrate thus resulting in similar spectral curves.
BLEACHED CORAL IN THE BACKREEF ENVIRONMENT.The final category considered is
bleached coral and sand in water depths of 3.5, 2.7, and 1.8 m as in Figure 6. Note that the
y-axis scale is different than the plots thus far since the magnitude of reflectance is con-
siderably higher for bleached coral and sand than the other substrates considered. In the
deepest water case (3.5 m), at wavelengths less than 551 nm, the surface measurements
are greater in magnitude than the bottom measurements, but at wavelengths greater than
551 nm, this relationship reverses. Interestingly, in the shallower water examples (2.7 and
1.8 m), the measurements taken at the surface are consistently greater in magnitude than
those at the bottom. The spectral reflectance dip at 515 nm is visible on the surface curves,
as is consistent with the remainder of the data set.
To examine the differences at each wavelength between surface and bottom measure-
ments, the spectra measured at the top of the water column are subtracted from the spec-
tra measured at the bottom of the water column. The resultant spectra are compared in
Figure 7. At wavelengths greater than 590 nm, 100% of the differences are positive, so the
bottom measurements are greater in magnitude than the surface measurements in all cases.
696 BULLETIN OF MARINE SCIENCE, VOL. 69, NO. 2, 2001

Figure 6. Bleached coral and sand substrates are compared.

In six cases (35%), the differences are negative at wavelengths smaller than 590 nm.
These six cases, in order of greatest to smallest negative difference, include (1) rock and
algae at 3.9 m, (2) sand/rock and algae at 4 m, (3) coral and sand at 3.5 m, (4) bleached
coral and sand at 3.5 m, (5) coral and sand at 4.6 m, and (6) coral and sand at 2 m. The
range of depths is small (2.6 m), and the spectra are the shallowest of the data set, yet all
spectra measured in shallow water do not display negative differences in this wavelength
region, indicating that this spectral feature is not necessarily depth dependent. A common
substrate type present for five of the six cases is sand, so perhaps the brightness of this
substrate contributes to multiple reflectance in the shorter wavelengths thus allowing more
light to be available for measurement at the surface. This possibility is also supported by
the fact that these six cases were measured in shallow water where multiple reflectance of
light within the water column is predictable. The observation that this phenomenon is not
present in all cases is confounding, but perhaps several factors must act in combination
such as sufficiently shallow water and bright substrate.
Another observation of the difference spectra is that three cases display steep declines
between 580 and 600 nm, but the difference spectra do not drop below zero. These three
spectra are (1) seagrass at 5.4 m, (2) dead coral at 7.8 m, and (3) sand and algae at 11.7 m.
The sharp decline in difference indicates that at wavelengths shorter than 580 nm, the
bottom measurements were significantly higher than the surface measurements, but at
wavelengths longer than 600 nm, the difference is negligible or nothing. These spectra
were measured at among the greatest depths in the data set, so this phenomenon may be a
function of deeper water. This explanation is feasible since it is expected that there will be
increased absorbance by the water in the longer wavelengths.
 HOLDEN AND LEDREW: HYPERSPECTRAL REFLECTANCE OF SUBMERGED CORAL REEF FEATURES 697

Figure 7. The difference spectra are a result of subtracting the surface spectra from the bottom
spectra.

SUMMARY AND DISCUSSION

There is a characteristic dip in reflectance at approximately 515 nm on the spectral

curves measured at the top of the water column that is not present on the curves measured
at the bottom of the water column. This spectral dip is present regardless of the depth of
water over which measurements were taken, and is therefore likely a function of absor-
bance by water column constituents or the water itself.
While attenuation of light energy appears to decrease in intensity from the surface to
depth following Beers Law of exponential decay in the longer wavelengths, the situation
is inconsistent in the shorter wavelengths and does not appear to be dependent upon water
depth or substrate type. Even though it is expected that 2-flow (down and then back up the
water column) attenuation would result in lower magnitude of spectral reflectance at the
top of the water column, in some cases the reflectance at the top of the water column is
greater in magnitude than at the bottom. This has great implication when devising algo-
rithms to account for attenuation in the water column on remotely sensed imagery of
submerged coral reef ecosystems. A model expressing logarithmic extinction of light at
all wavelengths regardless of water depth is not appropriate, as shown here, and a more
complex approach is required.
It appears that common water column correction procedures involving subtraction of a
deep-water reflectance value may not be appropriate for hyperspectral remote sensing
due to the wavelength-specific, complex and variable effects of the water column. Sub-
tracting a deep-water value from each pixel assumes that energy traveling through a water
column behaves the same way regardless of substrate type and water depth. To suggest
that a correction algorithm be substrate-specific is nonsensical for mapping applications
where the goal is to identify substrate type, for such algorithms would require identifying
the substrate before the correction is applied. Furthermore, while it is possible to create
an accurate digital elevation model (DEM) to overlay on the image providing brightness
and depth information for each pixel, this is an expensive and technologically advanced
procedure that may not be feasible for many projects.
698 BULLETIN OF MARINE SCIENCE, VOL. 69, NO. 2, 2001

ACKNOWLEDGMENTS

The National Oceanic and Atmospheric Administration, National Ocean Service Center for Coastal
Monitoring and Assessment supported data collection in the U.S. Virgin Islands. This research was
also supported by an NSERC operating grant to E. LeDrew and an NSERC graduate scholarship
and Canada Center for Remote Sensing scholarship to H. Holden. We owe great thanks to the field
research assistance of C. Derksen, B. Kalbfleisch, C. Newman, and the support staff at Buck Island
National Monument.

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