Freshwater Biology (1999) 41, 373±391

The importance of physical habitat assessment for

evaluating river health
IAN MADDOCK
Department of Geography, University College Worcester, Henwick Grove, Worcester WR2 6AJ, U.K.

SUMMARY

1. Physical habitat is the living space of instream biota; it is a spatially and temporally
dynamic entity determined by the interaction of the structural features of the channel and
the hydrological regime.
2. This paper reviews the need for physical habitat assessment and the range of physical
habitat assessment methods that have been developed in recent years. These methods are
needed for assessing improvements made by fishery enhancement and river restoration
procedures, and as an intrinsic element of setting environmental flows using instream flow
methods. Consequently, the assessment methods must be able to evaluate physical habitat
over a range of scales varying from the broad river segment scale (up to hundreds of
kilometres) down to the microhabitat level (a few centimetres).
3. Rapid assessment methods involve reconnaissance level surveys (such as the habitat
mapping approach) identifying, mapping and measuring key habitat features over long
stretches of river in a relatively short space of time. More complex appraisals, such as the
Physical Habitat Simulation System (PHABSIM), require more detailed information on
microhabitat variations with flow.
4. Key research issues relating to physical habitat evaluation lie in deciding which levels of
detail are appropriate for worthwhile yet cost-effective assessment, and in determining
those features that are biologically important and hence can be considered habitat features
rather than simple geomorphic features.
5. The development of new technologies particularly relating to survey methods should
help improve the speed and level of detail attainable by physical habitat assessments.
These methods will provide the necessary information required for the development of the
two-and three-dimensional physical and hydraulic habitat models.
6. A better understanding of the ways in which the spatial and temporal dynamics of
physical habitat determine stream health, and how these elements can be incorporated into
assessment methods, remains a key research goal.

Keywords: physical habitat, assessment methods, river health

Introduction been aligned for farming convenience, to aid naviga-

Rivers throughout the world have suffered a long
history of degradation through direct and indirect
human influence. Channel modification has been both
widespread and intensive as streams and rivers have
Correspondence: I. Maddock, Department of Geography, Uni-
versity College Worcester, Henwick Grove, Worcester WR2 6AJ,
U.K.
E-mail: i.maddock@worc.ac.uk
tion, to achieve the engineering objectives of flood
alleviation and agricultural drainage or straightened
adjacent to roads and railways. As a consequence,
many rivers have a `channelized' nature with straight,
trapezoidal channel sections, clear of river bank trees
and hedges and with uniform bed morphology
(Brookes, 1988). Flow regulation and modification
have also been widespread. The quantity and timing
of water movements have been altered through the
impacts of direct abstractions from the channel for

ã 1999 Blackwell Science Ltd. 373

374 I. Maddock
irrigation and industrial purposes, through the con-
struction of dams and reservoirs for water supply,
flood reduction and hydropower generation, and
through the use of rivers as open pipelines to transfer
water between drainage basins (Petts, 1984). Changes
in water quality are also common, particularly in
lowland areas where the impacts of agriculture and
urbanization are most widespread (Sweeting, 1994).
The combined effects of pollution, channelization
and river regulation mean that rivers that could be
considered natural are indeed a rare phenomenon.
The deleterious effects of these impacts from a
conservation perspective have been widely documen-
ted. Changes in water quantity, water quality and the
physical structure of the channel have almost without
fail led to changes in the composition of the biotic
community inhabiting the river, usually with a
reduction in the biological diversity of the aquatic
ecosystem (Boon, 1992).
More recently, recognition of the adverse effects of
human impacts on river systems, coupled with a rise
in environmental awareness, has driven initiatives for
river restoration as part of river management
schemes. Some river restoration initiatives aim to
improve the water quality (Jordan, Gilpin & Aber,
1987) whereas others aim to improve the ecological
integrity of river systems (RRP, 1993). Programs for
channel restoration have also been motivated from an
engineering viewpoint because channelized rivers
have often been unstable, with the need for expensive
mitigation measures or maintenance. Techniques of
river rehabilitation such as re-creating pools and
riffles, reinstating meanders in straightened reaches,
artificially narrowing over-wide channels, placing
structures on the bed to create morphological diver-
sity and breaking-out concrete channels and culverts,
are now beginning to be applied in many countries.
Whatever the driving force, there is a growing body of
knowledge relating to the scientific theory, techniques
and successful applications of river restoration being
applied across the globe (Brookes & Shields Jr., 1996).
This combination ± the recognition of the deleter-
ious effects of river regulation, channelization and
pollution, coupled with a move towards more
environmentally sensitive river management and
river restoration ± has created a demand for methods
which (1) examine the existing condition or `health' of
river systems, and (2) identify the conditions that may
have been expected had there been no impact.
The condition or health may be influenced by a
number of factors relating to the river, including its
ecological status, water quality, hydrology, geomor-
phology and physical habitat. Tools have been
developed for identifying and assessing each of
these components.
An analogy can be drawn between methods of
diagnosing river health and methods commonly
applied to human health assessment. For example, a
doctor wishing to assess the health of a patient may
check several indicators, such as pulse, breathing,
temperature, the patient's reactions and the blood
content. The doctor will use a specific measure of each
indicator, such as the pulse rate per minute, or the
oxygen levels, sugar levels and red blood cell count of
a blood sample, and compare the measurements
against the expected normal or healthy values (bench-
marks). We may also expect the doctor to diagnose the
likely source of the problem when certain indicators
are not normal, and prescribe a course of treatment to
improve the patient's health. Therefore, a proper
review requires a check on not just one but a number
of these diagnostic tools. The same is true for
assessing river health. The indicators include the
ecological status, water quality, hydrology, geomor-
phology and availability of physical habitat. To check
these indicators of river health, specific measures
must be addressed within each, such as biotic
diversity, flow regime or evidence of channel instabil-
ity (Fig. 1). Assessing physical habitat is an important
member of this suite of indicators.
Appraisals of the condition of a river may incorpo-
rate an evaluation of its ecological status, i.e. the
presence and condition of the biota in the river. This
could involve examining any one or more of the algae,
macrophytes, invertebrates or fish. Assessment may
involve an examination in terms of species diversity,
numbers of individuals, biomass, community struc-
ture, or a summary index incorporating more than
one of these (Rosenberg & Resh, 1993). Similarly water
quality may be examined by looking at the levels
and/or concentrations of individual constituents of
the water (e.g. nitrates, pH, phosphates) or use of an
index that integrates a number of parameters: for
example, the River Ecosystem Classification. This is a
system for classifying the quality of rivers and canals
used by the Environment Agency in England and
Wales. It comprises five hierarchical classes in order
of decreasing quality, and is a summary index based
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Fig. 1 The analogy between diagnostic tools for assessing human
health and river health.
on measurements of dissolved oxygen, biochemical
oxygen demand, total ammonia, un-ionized ammonia,
pH, hardness, dissolved copper and total zinc (The
Surface Water Regulations, 1994). The hydrologic
regime has also been recognized as playing an
important role in determining the biotic composition,
structure and function of aquatic ecosystems. Recent
developments have attempted to define ways of
characterizing flow regimes based on biologically
relevant attributes (Poff & Ward, 1989) and assessing
the extent to which these have been altered by human
influence. Important hydrologic parameters that can
be used to identify the degree of biologically relevant
flow alteration (Richter et al., 1996) include flow
magnitude, the magnitude, duration and timing of
annual extreme conditions, frequency and duration of
high and low pulses, and the rate and frequency of a
change in flow conditions.
Each of the assessments above focuses on a
different component that influences ecosystem integ-
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391
Physical habitat assessment 375
rity, and each is useful for providing an inventory of
the existing condition or health of the river. They may
also be used for planning management activities, and,
when compared to the conditions expected without
human impacts, they facilitate the identification of
goals for restoration and rehabilitation purposes.
However, methods for evaluating water quality,
water quantity and biological quality are fairly well
established compared to those designed to assess
physical habitat. The lack of a comparable method to
describe and assess the physical habitat of rivers has
started to be addressed, and physical habitat is being
incorporated as a basic element for the assessment of
the status of river systems (NRA, 1996). The following
section introduces its importance in determining river
health.
What is physical habitat and why is it important?
Publications concerned with aquatic habitat have
increased in recent years in association with a move
towards environmentally sensitive river management
and river restoration. The role of flow and channel
morphology in determining the structure of river
ecosystems received little attention until the early
1980s (Newbury, 1984; Nowell & Jumars, 1984).
However, probably because of its fairly ubiquitous
use, very few publications actually define the term
`physical habitat'. Jowett (1997) has recently suggested
that the generic term `habitat' is used to describe the
physical surroundings of plants and animals, and
therefore aquatic habitat can be defined as the local
physical, chemical and biological features that pro-
vide an environment for the instream biota. It is
affected by instream and surrounding topographical
features, and is a major determinant of aquatic
community potential (Aadland, 1993). There is con-
siderable evidence to suggest that both the quality and
quantity of available habitat affect the structure and
composition of resident biological communities; hence
the importance of physical habitat is clear (Hynes,
1968; Ward & Stanford, 1979; Meffe & Sheldon, 1988;
Calow & Petts, 1994). It is also important to recognize
that the term habitat implies some biological signifi-
cance, and that it is not simply an identifiable physical
feature.
The importance of physical habitat in determining
the condition of the river ecosystem is implicit in its
definition, because without a suitable `living space' a
376 I. Maddock
Fig. 2 The concept of habitats as the natural link between the
environment and its inhabitants (Harper et al., 1995).
given species is unlikely to exist at that particular
location. Indeed, it was recognized by Stalnaker (1979)
that the productivity of any stream system is likely to
be determined by four key factors, namely water
quality, the energy budget (e.g. the temperature
regime, organic matter, nutrients), the physical struc-
ture of the channel, and the flow regime.
Based on these factors a combination of the last two
produces the physical habitat for the instream biota.
Indeed, physical habitat is a particularly useful
element to be considered for evaluating river health
since it provides the natural link between the physical
environment and its inhabitants. This was illustrated
by Harper, Smith & Barham (1992) (Fig. 2) who
identified physical habitats as fundamental units on
which to base river conservation recommendations.
River channels are made up of structural features
(e.g. channel size, channel shape, gradient, bank
structure, substrate size). When these features are
combined with a particular discharge level, a distinct
pattern or mosaic of hydraulic features (depths,
velocities, shear stresses) is produced. It is a combina-
tion of these two attributes that make up the physical
habitat (Fig. 3). Consequently, physical habitat is
dynamic both in space and in time. At any one time
the bed morphology and river flows are likely to vary
longitudinally and so the quantity and quality of the
physical habitat changes in this direction. Also,
variation is present in the lateral direction (e.g. from
bank to bank or from one edge of the floodplain to the
other) and vertical direction (e.g. from the hyporheic
zone to the water surface). A fourth dimension is
apparent as the flows in a river may change over the
short and longer time scales in response to individual
storm events and seasonal climatic influences. The
Fig. 3 Physical habitat determined by the interaction of
geomorphology and hydrology.
channel morphology may also be susceptible to
change over time, but perhaps less frequently than
the discharge component.
The need for physical habitat assessment and the
importance of scale
The demand for procedures to assess physical habitat
has been driven from a number of different quarters.
Fishery enhancement methods, i.e. placing structures
in rivers to increase the habitat available to fish, have
required techniques to assess and quantify their level
of success (Swales, 1989). River restoration programs
have required tools to assess the present stream
resource within selected stretches of river so their
physical habitat availability can be compared before
and after restoration has taken place, and the
effectiveness of the schemes can be appraised (Hvid-
sten & Johnsen, 1992; Habersack & Nachtnebel, 1995).
Instream (or `environmental') flow assessment meth-
ods commonly involve determining the effect of
existing or proposed flow regimes on habitat provi-
sion for selected target species; they have required the
development of techniques to quantify physical
habitat (Petts & Maddock, 1994).
In addition to each of these methods having
different data requirements, many are applied over
various spatial scales. Fishery enhancement methods
may require appraisals of individual structures;
restoration projects may operate along short stretches
of river; environmental flow evaluations may require
many kilometres of river to be assessed in terms of
flow vs. physical habitat relationships. The scale of
approach to river investigations can be considered
from the microhabitat level up to the catchment scale
(Fig. 4) (Frissell et al., 1986; Petts, 1994). A river may
be examined across a spectrum of scales which can be
ordered into a hierarchy, each with a different degree
of sensitivity and recovery time. They form a system
that not only defines the structural components of a
river, but also recognizes that the factors controlling
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 Physical habitat assessment 377

Fig. 4 A functional classification of rivers based on scale (after Frissell et al., 1986; Petts, 1984).

the short-term and long-term behaviour of streams
change in relative importance at various spatial scales
(Maddock & Bird, 1996).
An example of recognizing different spatial scales
was highlighted by Muhar (1996). She used a
modified hierarchy of scales based on the work by
Frissell et al. (1986) and Naiman et al. (1992) to
identify the range of restoration measures and fish
habitat improvements that could operate at each of
these levels. Table 1 illustrates these spatial scales and
the restoration measures and fish habitat improve-
ments that might operate at each level based on
examples from Austria.
Reach or segment scale
At the reach or segment scale, the environment is
relatively stable and biota are determined by the

Table 1 Restoration measures and fish habitat improvements in relation to spatial scale (Muhar, 1996)

Spatial scale/system level Restoration measure Fish habitat improvement

MICROHABITAT:, e.g. zones of
varying substrates, water depths
and current velocities within the
river channel
MACROHABITAT: pool/riffle sequence
within the bank full channel
REACH: river channel and floodplain
within a 1±5 years floodplain
SEGMENT: river channel and
complete floodplain
characterized by the same river type
STREAM-SYSTEM part of the catchment
area characterized by different river types
Installation of single structures in
order to create substrate and velocity
diversity (e.g. boulders, tree stumps,
pilings, small groynes)
Installation of a series of groynes,
initiation of pool/riffle sequences;
river bank enhancement
Creation of meanders; initiation of
channel widening
Widening of the river bed in order to
initiate braided or meandering river
segments; large scale excavation of
floodplain alluvium along severely
entrenched river channels
Removal of man-made obstructions
to fish migration and sediment
transport (dams, torrent control
devices, etc.)
Improves conditions for specific life cycle
stages of riverine species (e.g. spawning,
substrate or larval refuges for salmonids
and rheophilic cyprinids)
Ideally creates the full set of conditions
for the complete life cycle of individual
riverine species (brown trout) as well
as for the integrity of the fish community
An increase in the habitat available for
species utilizing both the main channel
and floodplain for the completion of
their life cycle (pike various cyprinids)
Fulfilment of habitat requirements for all
species living within these braided and
meandering segments, including the lateral
connections within the floodplain
Fulfilment of habitat requirements for
species utilizing the entire stream system
(e.g. anadromous Acipenseridae)

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378 I. Maddock
overall features of the region, its topography and
altitude and its geomorphic or land use pattern. This
in turn produces a broad pattern of hydrology,
temperature and chemistry. Dominant substrate,
channel gradient, landform feature, sinuosity, and
width/depth ratio are measured to determine discrete
reaches.
Macrohabitat or mesohabitat
At this scale the physical habitat units are at an
intermediate level and hence are most commonly
termed mesohabitats. The distribution of habitat types
within reaches has not received as much attention in
the literature. Bisson et al. (1982) focused awareness
on habitats as channel units by creating typologies
based on hydrological and geomorphological features,
followed by an examination of fish distributions
among these habitats (Bisson, Sullivan & Nielsen,
1988). At this scale of approach, habitat features of
different river sections such as average flow velocity,
morphological type (e.g. riffle, pools) and bankside
cover are deemed influential. Typical mesohabitats
used in these studies include riffles, cascades, pools,
glides and runs. The idea that distinct mesohabitats
exist in streams has been recognized for some time yet
most studies have developed their own typology to
suit the particular river in question or the species that
is being investigated. For example, Brooker (1981)
identified the habitat types present in the River Teifi
whereas Kershner & Snider (1992) used the habitat
typology developed by Bisson et al. (1982) and
identified 18 habitat types that were present in their
study of the Truckee River in California and Nevada.
Table 2 illustrates the large number of different
mesohabitat types that have been identified by just
these two studies alone.
This simple comparison of just two studies is
typical of the difference in mesohabitat types identi-
fied between applications. Some features are evident
in one typology and absent in the other (e.g. cascade
or slack); some features are defined as a single feature
in one typology but are subdivided into further
categories in the other (e.g. single pool category vs.
trench, plunge, lateral scour, dam-pool categories,
etc.); and others features are common to both (e.g.
backwater). This example also demonstrates how
some mesohabitats may be defined based on geo-
morphic units, yet habitats may also be based on
aquatic plants (e.g. Callitriche spp.) or riparian
terrestrial vegetation (e.g. tree roots).
Other mesohabitats have also been based on
substrate sizes (e.g. Barmuta, 1989). Due to the
geographical variations in river morphology and the
fact that different studies target different species for
identifying habitats it is hardly surprising that
numerous mesohabitat classifications have been
used and that there is no definitive mesohabitat
typology available.
Microhabitat
Habitat also includes the distribution of hydraulic and
structural features comprising the actual living space
of the organism at a much smaller scale called
microhabitat (Bovee, 1982). For instance, the exact
positions chosen by resident salmonids appears to be
related to small scale physical characteristics, espe-
cially depth, velocity, substrate and cover (Lewis,
1969; Shirvell & Dungey, 1983; Kershner & Snider,
1992). Brown trout were found to prefer distinct
velocities according to whether they were feeding or
spawning and chose similar microhabitats regardless
of the available habitat in different rivers (Shirvell &
Dungey, 1983).
Physical habitat assessment methods
A number of approaches have been developed in
recent years that incorporate an element of physical
habitat assessment. Some have been developed
particularly for this purpose, whereas others have
set out to assess the geomorphology or biota present
within a river system and have incorporated an
element of physical habitat as part of this. In the
same way that river investigations can be considered
as part of a hierarchy of scales, different habitat
assessment methods operate at different spatial levels
and some examples of these are summarized in
Table 3.
Broad scale assessments
Rosgen (1985) produced a reach-level classification of
river types based on objective criteria that were easily
measured (e.g. dominant substrate and sinuosity).
This has since been developed to provide a more
detailed guide for the classification, assessment and
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 Physical habitat assessment 379
Table 2 Examples of mesohabitat types identified by Brooker (1981) and Kershner & Snider (1992)

Mesohabitat type Mesohabitat type

primary descriptor secondary descriptor Physical description

Cascade* Swift current, exposed rocks and boulders, high gradient and
considerable turbulence, consisting of a stepped series of drops
Riffle* Shallow rapids, high current velocity, disturbed surface,
partially submerged obstructions
Low gradient riffley See above (low gradient)
High gradient riffley See above (high gradient)
Glidey A slow moving shallow run with calm water and little or
no surface turbulence
Runy Step runy An area of swiftly flowing water without surface agitation or
surface waves
which approximates to uniform flow
Fast run* Similar current velocity to, but deeper than riffle
Slow run* Similar to fast run, but with reduced current velocity
Backwaterz Area of minimal current velocity, partially isolated from
channel during low flow
Edgewatery A backwater along the edge of the channel where the stream
is wider than above or below
Slack* Shallow bankside area of much reduced current velocity,
generally silty
Pool* Discrete area between faster reaches; velocity reduced,
depth variable
Trench pooly A long depression found in bedrock channels
Plunge pooly Created by water passing over a channel obstruction
Lateral-scour (tree)y Pool created as flow is directed to the side of the channel by
an obstruction (tree)
Lateral-scour (root)y See above (caused by a root)
Lateral-scour (bedrock)y See above (caused by bedrock)
Lateral-scour (boulder)y See above (caused by a boulder)
Dam pooly Upstream from a channel blockage, e.g. debris jam
Main pooly Standing water in the centre of the channel
Channel confluencey Pool created where the main channel meets a tributary
Corner pooly A backwater along the bank of a meander bend
Tree roots* Submerged fibrous system of alder, ash, sycamore and
willow in deep water
Grass roots (Phalaris)* Submerged fibrous systems of bankside stands
Ranunculus pencillatus* Extensive stands in regions of low current velocity, usually
at margins of channel
Callitriche spp.* Extensive stands in regions of low current velocity, usually
at margins of channel
Potamogeton natans* Extensive stands in regions of low current velocity, usually
at margins of channel

*Mesohabitat type identified by Brooker (1981).

yMesohabitat type identified by Kershner & Snider (1992).
zMesohabitat type identified by both studies.

monitoring of rivers (Rosgen, 1994, 1996). Stream
reaches are first delineated into one of nine types
based on channel slope, channel pattern (e.g. mean-
dering, braided, anastomosed), and channel cross-
sectional shape called the geomorphic characteriza-
tion level. Each of the nine types is further subdivided
at level 2 based on morphological description using
measures of entrenchment, width/depth ratio and
channel materials. The stream `state' or `condition' is
addressed at level 3 and assesses current stability,
potential and function with a view to comparing this
with its expected natural state. A fourth level is
designed to establish empirical relationships between
reach conditions and sediment condition, stream flow,

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380 I. Maddock
Table 3 A summary of the physical habitat assessment methods used to evaluate stream health
Assessment type Approach
Broad scale Involves delineation of the stream system
assessments into shorter segments, types or reaches based
on physical characteristics. Initial division is
often based on features such as channel slope,
channel pattern, geology, surrounding land use
and/or hydrological regime identified from map
sources and/or historical data.
Microhabitat Uses analysis of small scale variables such as
assessments substrate, cover, water depth and current
velocities to identify the quantity and quality
of the physical habitat available for selected
target species
Empirical Regression models are developed to predict
habitat biological characteristics based on measurement
models of existing physical features
and stability so that they can be used to improve the
predictive capability of the approach.
Miller & Ritter (1996) have applauded this classifi-
cation of physical habitat at the reach scale as a
communications tool but have criticized the sugges-
tion that the classification may be used for predicting
fluvial processes. They argue that the current level of
understanding of reach response to changes in the
controlling factors (e.g. climate, tectonics and land
use) is insufficient to enable predictions of the type or
magnitude of geomorphic response.
The River Habitat Survey (RHS) methodology being
developed in the UK by the Environment Agency
involves recording the physical structure of the river
channel, its banks and adjacent land use over 500 m
stretches of river (Fox, Naura & Raven, 1996). A
stratified random sample of 3400 sites throughout the
UK had been sampled by December 1995 and
compiled onto a computer database. Nine river
types were derived from the data based on geology,
gradient and land use. The database now enables
independent river reaches to be assessed using the
established survey methodology, and the physical
features that are recorded for the given river type can
be compared with those present at the existing
`seminatural' sites on the database. One of the
drawbacks of national databases such as this is that
they lack the precise definition required for individual
rivers and can be expensive to create and maintain.
However, the lack of precise definition can be
outweighed when they provide a predictive ability.
Large-scale programs also have the vital function of
Spatial scales addressed Examples
Drainage basin to Rosgen classification (Rosgen, 1996)
reach level River habitat survey (Fox et al., 1996)
Reconnaissance level survey
(Thorne & Easton, 1994)
Habitat mapping
(Maddock & Bird, 1996)
Reach to patch scale PHABSIM (Bovee, 1996)
Bioenergetics models
(Hill & Grossman, 1993)
Reach to patch scale Habitat quality index
(Binns & Eiserman, 1979)
HABSCORE (Milner et al., 1985)
allowing any detailed study to be viewed in a broader
geographical context (Harper et al., 1995). Within the
RHS, comparison between a selected site and the
existing database enables the physical features of the
site to be assessed as typical, natural or possibly
impacted in some way compared to the national or
regional picture, or by river type.
Thorne & Easton (1994) designed a reconnaissance
level survey method to standardize the types of
habitat observations that geomorphologists or stream
ecologists may make routinely, but that are not
usually recorded in such a disciplined way. They
stated that this information was needed to provide a
scientific and repeatable method for observing and
interpreting channel morphology and instream habi-
tat. It would aid with the supply of useful information
for schemes to rehabilitate and restore geomorphic
features in engineered streams, and highlight those
features that need to be conserved in natural systems.
Downs & Brookes (1994) developed a method for
the appraisal of river projects by assessing the current
status of the geomorphology using information on the
valley characteristics (e.g. floodplain land uses),
channel characteristics (e.g. bank and substrate con-
dition) and channel dynamics (e.g. morphology and
the presence of instream structures). For this method
the rest of the catchment must be assessed, using
geological, soil survey and topographic maps, as well
as the selected reach that is the focus of the
investigation, because commonly it is factors that
operate beyond the specific reach that determine the
success or failure of the restoration project. However,
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these survey methods are distinct from physical
habitat survey tools. Although the methods survey
physical features, they do not necessarily identify
their ecological value as habitat units: rather they
record information on the physical features present
and the geomorphological status of the channel and
its surrounds. Habitat mapping techniques, however,
involve identifying physical features that have an
intrinsic ecological value.
Habitat mapping surveys incorporate a mixture of
qualitative assessment and physical measurement to
create a record of the form of a river, based on field
observation (Bisson et al., 1982). The surveys involve
walking the appropriate sector of river, identifying
mesohabitats, noting their location and extent, and
measuring their physical attributes, e.g. water
width, depth, velocity, etc. A classification of
mesohabitat types should be chosen before com-
mencing the fieldwork. This can either be based on
professional judgement, or taken from the various
sources available in the literature (e.g. Bisson et al.,
1982; Rosgen, 1985; Modde, Ford & Parsons, 1991),
or both. Ecological studies may also attempt to
describe the physical features that are biologically
relevant to the resident biota. The typology may
also be refined after completion of the fieldwork, to
incorporate river-specific circumstances. In other
words, some types may be merged to simplify the
typology if the original method was more complex
than necessary (e.g. combining intermediate glides
with deep glides to give a single deep glide
category). Others may have to be subdivided to
account for within-stream variability not recognized
by the original types (e.g. subdividing pools into
plunge pools, lateral pools and scour pools). These
decisions must take account of the trade-off between
creating a typology that has too many mesohabitats
and is cumbersome to apply, and one that has too
few and may omit an important category of
mesohabitats. This information can then be used to
identify the longitudinal distribution and total
length/area and proportional length/area of each
mesohabitat within the study sector.
Habitat mapping methods place the emphasis on
using minimal time and effort to cover long stretches
of river and therefore must forego some of the detail
and accuracy that are associated with more quantita-
tive techniques applied at the microhabitat level.
Nevertheless, by including an element of physical
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Physical habitat assessment 381
measurement they are more precise than subjective
intuitive assessment, and allow field analysis to be
undertaken at the segment scale rather than at the
smaller reach scale.
Microhabitat assessments
The Instream Flow Incremental Methodology (IFIM)
was developed under the guidance of the US Fish and
Wildlife Service and is a method that attempts to
integrate the planning concepts of water supply,
analytical models from hydraulic and water quality
engineering, and empirically derived habitat vs. flow
functions. The Physical Habitat Simulation System
(PHABSIM) is a computer-based model that is part of
the IFIM (Milhous, Wegner & Waddle, 1984). It is
based on field measurements of channel shape, water
depth, velocity and substrate. When combined with
hydraulic modelling and a knowledge of the habitat
requirements of selected target species, the model will
produce simulations of the quantity and quality of
existing habitat vs. flow relationships based on
existing conditions, and of `potential habitat' resulting
from proposed water development (Stalnaker et al.,
1994). Physical habitat availability is initially calcu-
lated on a point by point basis and hence at a
microhabitat level. These data are then combined to
provide values over broader scales.
The developers of PHABSIM advocate three levels of
assessment (Bovee, 1982). Firstly, the river is divided
into segments (typically a few kilometres in length)
which are defined by variables that instigate changes in
geomorphology, hydrology and/or water quality, e.g.
where changes in geology are evident, at tributary
confluences, or the location of significant abstractions
or augmentations. Within each segment, water quality,
sediment load, and hydrological regime are seen as
largely invariant. Secondly, each segment is divided
into representative reaches (typically a few hundred
metres in length) on the basis of local variations in
channel morphology or river-margin vegetation. Var-
iations between individual reaches within a segment
relate to local conditions (bank sediments, riparian
vegetation, etc.). On this basis, PHABSIM involves
measurement across transects at the reach scale.
Measurements at individual points across each transect
based on water depth, velocity, substrate and cover are
then used to describe the microhabitat conditions
within the selected reach (Petts et al., 1995).
382 I. Maddock

Fig. 5 The basis of PHABSIM (after Nestler et al., 1989) showing the integration of hydraulic measurements and habitat suitability
criteria to define the flow vs. habitat relationship. This can be combined with a flow time series to produce a habitat time series and
habitat duration curve.

The standard output of a PHABSIM assessment is a
flow vs. physical habitat relationship for each reach
and target species under investigation (Fig. 5). This
can in turn be combined with a historical flow time
series to produce a physical habitat time series and
hence a physical habitat duration curve. Alternative
flow management scenarios filtered through this
process will allow a comparison of the effects of
different flow regimes (e.g. actual vs. proposed) on
physical habitat availability (Petts & Maddock, 1994).

ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391


It has long been recognized that to enable reach-
specific physical habitat results to be applied and
extrapolated to a longer sector of the river, it is first
necessary to undertake a `habitat mapping' or
`reconnaissance level' survey at the sector level
(Bovee, 1982; Rabeni & Jacobson, 1993). However,
many studies have neglected this initial sector-level
analysis and reaches have been selected on a profes-
sional judgement basis rather than on quantitative
data. This in turn leads to difficulties in extrapolating
reach results with any degree of certainty to larger
stretches of river. Habitat mapping should be under-
taken before PHABSIM transects are selected for field
data collection, because the habitat mapping data can
be used to identify the number and types of
mesohabitats that should be sampled so that the
data collection is truly representative, and can direct
the field operators to the locations of these mesoha-
bitats. This in turn allows the results from a more
detailed appraisal to be extrapolated back to the large
scale where management recommendations are more
appropriate (Maddock, Petts & Bickerton, 1995;
Maddock & Bird, 1996).
A method for assessing physical habitat at a range of
spatial scales was developed by Maddock et al. (1995).
The river was delineated into types and sectors, based
on map sources, hydrological data, and biological
records for fish and invertebrates. A habitat mapping
survey and the collection of additional hydrological
data subsequently allowed the physical habitat to be
appraised in more detail within each sector. These data
were also used to select representative reaches and
transects for a PHABSIM study that quantified
physical habitat availability for two life stages (juve-
nile and adult) for the dominant species, dace
(Leuciscus leuciscus) and chub (Gila spp.), and a target
species for the river, brown trout (Salmo trutta). The
results from the PHABSIM study could then be
extrapolated up to the sector scale with the knowledge
that management recommendations were being pro-
posed in appropriate places and at an appropriate
scale (Petts et al., 1995). This provides an example of
how a range of physical habitat assessment methods
can be integrated across a spectrum of spatial scales.
Identifying biologically relevant physical fea-
tures
Some geomorphological survey methods have been
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391
Physical habitat assessment 383
developed to assess the current physical structure of a
channel and its surrounding floodplain, with a view
to providing an inventory of these features and
perhaps using this information to determine the
stability of the selected reach. However, a physical
habitat assessment method must demonstrate that the
physical features that are being measured are indeed
of ecological significance.
To define which features are influential in deter-
mining habitat quality, some studies have used an
empirical model approach to the study sites. Binns &
Eiserman (1979) developed a model to relate habitat to
standing crop for coldwater trout streams, with a high
degree of success. The study developed the Habitat
Quality Index (HQI), two regression models that
related 11 habitat variables that represent food,
shelter, streamflow variation and maximum summer
stream temperature to trout biomass density in
Wyoming streams. Each variable in the model was
rated with respect to its quality to trout from 0 (worst)
to 4 (best) according to a rating schedule. Both models
performed well in predicting trout biomass density in
Wyoming streams with model 1 explaining 35% and
model 2 explaining 86% of the variance. However, a
weakness of such an approach was highlighted by
Bowlby & Roff (1986) when they tested the models in
Ontario. Model performance was very weak which
suggested that some habitat variables play different
roles in limiting trout populations in Wyoming than
in Ontario.
A similar approach has been used by Milner,
Hemsworth & Jones (1985). An empirical model,
called HABSCORE, was developed to evaluate sal-
monid fisheries in Wales. When applied to the area in
which it was developed, differences, between abun-
dance predicted from assessing habitat variables at
the site and actual abundance, explained variances of
up to 93.6%. Other studies have applied similar
approaches and met with varying degrees of success
(e.g. McClendon & Rabeni, 1987; Modde et al., 1991).
Problems are thought to arise in identifying the key
habitat parameters that determine carrying capacity
and in devizing an appropriate way of measuring the
important habitat attributes. These approaches have
also tended to focus only on fish species which are
region-specific. Nevertheless, this type of approach
can still be a very useful tool in determining the
important physical habitat variables (and also hydro-
logical or chemical variables) that determine the
384 I. Maddock
instream biota. This information can then be incorpo-
rated into the types of data and habitat information
that are recorded during rapid assessment methods,
habitat mapping, or reconnaissance level surveys.
One problem associated with physical habitat
assessment is the need for objective and repeatable
field identification. Accurate identification of distinct
habitats in the aquatic and riparian zones often has a
subjective element. Part of the reason why there is so
much management information for habitats is that
they can be easily recognized, visually, from the river
bank, whereas many species and most ecological
functions cannot. Nevertheless, the effectiveness of
habitat-based recording of the natural environment
depends on the ability of the surveyors to consistently
see and recognize habitat units (Harper et al., 1995).
Pools and riffles are two mesohabitats that have
received, perhaps, the most attention from a geomor-
phological (Richards, 1976) and ecological perspective
(Scullion et al., 1982; Glova & Duncan, 1985). Various
features have been suggested for objectively delineat-
ing these features in the field, such as bed material
size, water surface slope and bed topography
(Richards, 1976; O'Neill & Abrahams, 1984). Defini-
tions based on bed topography may be more appro-
priate descriptors than hydraulic definitions, as they
change less with discharge. However, Jowett (1993)
identified pool, riffle and run type mesohabitats with
a success rate of 65±66% based on simple measure-
ments of water surface slope and either velocity/
depth ratio or Froude number.
A further challenge facing physical habitat assess-
ment methods is the trade-off between collecting
enough information to describe the physical habitat
characteristics along the reach, and making the
procedure too cumbersome and time consuming.
Simonson, Lyons & Kanehl (1994) investigated the
importance of transect spacing when carrying out
more detailed physical habitat data collection, with a
view to determining the minimum transects sample
sizes and spacing needed to characterize habitat
features in Wisconsin streams. Their results suggested
that it is more appropriate to space transects in terms
of mean stream widths (MSW) rather than on a
random basis or simply at predetermined regular
intervals. On the narrower streams (< 5 m wide) » 13
transects spaced every three MSWs were required,
whereas » 20 transects were required spaced every two
MSWs on the wider streams (5±35 m wide).
A recent method of characterizing the longitudinal
variability of shape, size and slope of stream channels
using surveyed cross-sections has been proposed by
Western et al. (1997). The advantage of this method is
that it has been designed to enable the use of existing
cross-section-survey data to characterize the channel
morphology along the selected reach where insuffi-
cient resources may restrict the collection of addi-
tional data.
Discussion
PHABSIM has been a useful and popular river habitat
assessment tool over the past two decades. Recent
studies have highlighted the potential of two-dimen-
sional and three-dimensional habitat models rather
than the one-dimensional approach of PHABSIM
(Bovee, 1996; Hardy, 1996). In other words, it is not
just the suitability of a particular location that needs to
be taken into account; the range of habitat types or
physical conditions that are adjacent to this point is
also important. For example, the spatial dynamics of
habitats have been demonstrated for fish ranging
from salmonids to paddlefish that require velocity
shelters associated with adjacent high velocity cur-
rents (Fausch & White, 1981; Southall & Hubert, 1984)
and small mouth bass require mid-channel pools or
runs that border pools that contain structural cover
(Rabeni & Jacobson, 1993). Incorporation of the idea of
patch dynamics within two-dimensional and three-
dimensional habitat models will therefore have dis-
tinct advantages over the one-dimensional techniques,
if the biological testing and validation can be
accomplished (Bovee, 1996).
The use of biological criteria for evaluating and
classifying stream systems is well established. One of
the commonest approaches using structural and
functional components of fish communities is the
Index of Biotic Integrity (IBI) developed in North
America by Karr (1981). The IBI is a sum of 12 metrics,
each scored as odd numbers up to 5, and includes
variables such as species richness and composition,
trophic composition, abundance and condition. These
are intended to identify the degree to which a
particular location is degraded from its natural state.
The Invertebrate Community Index (ICI) uses a
similar approach to evaluate biological integrity
using invertebrates (Ohio EPA, 1987). These indices
are intended to assess the environmental quality of
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391

stream reaches but they do not directly consider in-
channel physical features or extrinsic physical factors
which influence community structure. The funda-
mental premise of these approaches is that a range of
physical features control the structural and functional
attributes of communities and therefore the quality
and quantity of the physical habitat is reflected in the
index at any given site.
The US Environmental Protection Agency (EPA)
has developed a hierarchy of methods for biological
assessments of lotic systems, known as the Rapid
Bioassessment Protocols (Plafkin et al., 1989). The
protocols use fish and invertebrate assessments
similar to the IBI and ICI approaches and have also
incorporated a method for evaluating habitat quality.
A total of nine habitat parameters are scored for a
selected reach within three groups, i.e. substrate and
instream cover, channel morphology, and riparian
and bank structure. Maximum scores are higher for
those parameters in the first group and lower in the
latter group, to weight those attributes that are
considered to be the most important to the biological
communities.
Until recently, the different aspects that contribute
to river health (e.g. ecological status, geomorphology,
hydrology, physical habitat, water quality) have been
assessed as separate entities, leaving the river man-
ager with the problem of combining the results of
each of the different survey methods. However, more
appropriate methods of assessing river health would
aim to unify the assessment of each of these different
elements into a composite scheme.
One such approach that has attempted to develop a
method for integrating these various aspects is the
scheme that calculates an Index of Stream Condition
(ISC; Ladson et al., 1999). With appropriate weight-
ings, the ISC could adopt an approach similar to that
used in the physical habitat element of the Rapid
Bioassessment Protocols (Plafkin et al., 1989). The ISC
approach should be applauded for its incorporation of
an assessment of physical features beyond those
within the main river channel. A recognition of the
important influence of floodplains in contributing to
river health is apparent (Amoros, Roux & Reygrobel-
let, 1987), yet, to date, very few physical habitat
assessment methods have attempted to record the
nature of the physical features associated with the
floodplain environment and quantify their impor-
tance in any way.
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391
Physical habitat assessment 385
The need for physical habitat assessment is clear.
Considerable evidence links the quality and quantity
of physical habitat at a range of spatial scales and the
structure and function of indigenous biological com-
munities. The increasing environmental impacts
facing our rivers and the attempts to mitigate such
impacts through fishery enhancement procedures,
identifying instream flow requirements and insti-
gating river restoration projects, has driven the need
for physical habitat assessment methods. Many
approaches that examine stream health have focused
entirely on biotic indices (e.g. IBI, ICI) with the
implicit assumption that the resident communities
are determined in part by the quantity and quality of
the physical habitat, and that therefore an appraisal of
the habitat is inherent in the index or score provided
by the method. However, this approach is limited
because a poor biological score may be caused by poor
physical habitat quality, poor chemical quality,
biological factors such as predation or competition,
or a combination of these. Therefore, the indices do
not provide specific information to determine why a
stream's health may be poor. Other approaches (e.g.
Rapid Bioassessment Protocols, ISC) have attempted
to incorporate an index or score relating to the
physical habitat features without any substantial
evidence identifying why certain attributes are being
measured, why others are ignored, or to what extent
the physical features can be considered to be
biologically important. Therefore, one is left with the
sense that physical habitat assessment is included
because the developers recognize that it is an
important element in determining stream health, but
that it is largely an `add-on' in river condition
exercises. There is often no clear justification to
suggest why specific habitat features warrant mea-
surement and others do not.
One important element in the assessment of
physical habitat that has largely been ignored, to
date, is the comparison of the site or reach in question
with a reference, baseline or unimpacted site. The
RHS scheme described above (Fox et al., 1996) is
perhaps one exception to this where expected physical
features for the given reach can be compared with a
national database of features based on the nine stream
types. The classification of stream types is important
when comparing impacted sites with reference sites to
assess river health. If we take the analogy of human
health, then an average person's health may be
386 I. Maddock
perceived to be poor compared to that of an Olympic
athlete. Similarly, comparing the physical habitat of
river reaches to natural or healthy reference condi-
tions relies on a comparison to an appropriate river
type.
Irrespective of whether data are being collected on
mesohabitats at the larger segment scale, or micro-
habitat recognition at the reach scale, one of the most
limiting factors in physical habitat measurements is
the surveying time that is required. The need for
habitat assessment across a range of spatial scales is
recognized, yet large scale habitat mapping can be
very time consuming or simply not feasible if many
tens or even hundreds of kilometres require assess-
ment. At the other end of the spectrum, studies of
microhabitat variations can also require many hours
of detailed surveys. Recent developments suggest that
this problem will be alleviated to some degree by the
rapid development of new technologies.
The use of a theodolite with an electronic distance
meter (EDM) and automatic data logging facility was
reviewed by Parasiewicz (1996) based on its applica-
tion to 79 rivers in Austria, Switzerland and Germany
since 1990. This cuts out the time needed to set up
tape measures across the channel at every cross-
section of interest, set up the level with its horizontal
and vertical controls, manually record survey data in
the field and subsequently enter the data into a
computer for analysis at a later date. Downloading
data from the logger onto a notebook computer whilst
in the field allows rapid visualization of the field data
using an AutoCAD program. This can highlight errors
or omissions which may be corrected in the field,
avoiding expensive return visits to the site. The
method was deemed to be most successful on
relatively small wadable streams with fairly clear
water; the sampling time alone was reduced by an
estimated 70% of that taken for systematic sampling
using a level and staff.
The use of Global Positioning System (GPS)
technology for mapping, field data collection and
the construction of Geographic Information Systems
(GIS) across a range of disciplines is rapidly becoming
common (Cornelius et al., 1994; Fix & Burt, 1995;
Stafford, Le Bars & Ambler, 1996). The system is based
on a ground receiver accessing signals from at least
three orbiting satellites at a given time to calculate its
three-dimensional position (Van Sickle, 1996).
Single receivers that are commonly used for
hillwalking and trekking cannot overcome the degra-
dation of the satellite signals by the US government
(called `selective availability') and positions are only
obtained within 100 m of the truth 95% of the time
(Gilbert, 1993). For most investigations this is unlikely
to be accurate enough for mapping and relocating
physical habitat features. Differential GPS (DGPS)
combines a `base station' receiver in a fixed location
and a `rover' unit which is the receiver used in the
field to collect the locations and attribute data in the
field. The use of two receivers in this manner
counteracts the degradation of the satellite and
commonly allows locations to be mapped with an
accuracy of 2±5 m. Studies have linked DGPS survey-
ing technology with a hydroaccoustic data collection
system to collect a dense network of bed survey data
over relatively large spatial domains in a short space
of time (Gubala et al., 1994; Bartsch, Gubala & Hardy,
1996). These techniques are likely to become more
important when field data are required to simulate
physical habitat in the more complex two-and three-
dimensional hydraulic models being developed. This
combination of Sonar and DGPS has been demon-
strated to be effective in characterizing the precise
physical habitat of individual reaches and is likely to
improve understanding of the system attributes that
control biological diversity and river health (Gubala,
Eilers & Bernert, 1996). DGPS is also useful for rapid
assessments over longer reaches, i.e. for identifying
more accurate locations of start-and endpoints of
habitat features. In addition, attribute data associated
with these features can easily be exported to a GIS
program for additional analysis. The use of aerial
photography and aerial multispectral videography
have also been suggested as tools that will provide a
means of delineating mesohabitat features over long
stretches of river; these may otherwise be time
consuming to habitat map on the ground or perhaps
be totally inaccessible (Panja & Hardy, 1995).
These new developments may also help character-
ize physical habitat changes with flow. Single field
surveys of instream habitat over long reaches, such as
those used for habitat mapping, often rely on
assessing the river under a typical or representative
flow. This often falls within the medium to low flow
range when the physical habitat units are more
apparent and the field survey is safer. The develop-
ment of new technologies and more refined physical
habitat models will undoubtedly focus on the spatial
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391

and temporal aspects of physical habitat to a much
greater degree. This in turn may help bridge the gap
that exists between those approaches that focus on the
broad scale features of physical habitat and those that
concentrate on microhabitat features at a much
smaller scale.
A key challenge for the development of physical
habitat assessment in the future will be to understand
the numerous spatial and temporal elements of
physical habitat that determine the biotic commu-
nities, and incorporate them into appropriate methods
in a robust manner. The various spatial scales, from
the drainage basin to patch level, have already been
outlined (Fig. 3). Recent studies have tried to integrate
these spatial scales. For example, the work by Petts
et al. (1995) proposed a delineation of the drainage
basin into stream types and channel sectors, followed
by an appraisal of the mesohabitat composition in
each sector. A PHABSIM study along representative
reaches could then assess the physical habitat at the
small scale, with the results from this level extra-
polated up to the sector level for management
purposes. However, the accurate delineation of these
spatial scales and the various physical habitat features
that are identified has not been fully addressed.
The size or extent of different types of physical
habitat that are required to sustain a given number or
diversity of species is not properly understood, nor is
the extent to which the range of various combinations
and diversity of habitat types are biologically relevant.
For example, some approaches such as PHABSIM
quantify habitat availability, yet we do not fully
understand whether an increase or decrease in habitat
amounts by 10%, 20% or 50% is significant to
individuals or the community as a whole. This still
leaves decision-makers to use their own judgement
when determining when habitat loss, because of a
proposed development, becomes biologically signifi-
cant. The importance of the amount of contact zone or
edge between two physical habitat types and the
proximity of different habitat types has also been
highlighted by the development and application of
bioenergetics models (Hill & Grossman, 1993; Van
Winkle, Rovse & Chambers, 1993). It is hoped that
these will provide a better understanding of the
importance of the spatial dynamics of physical
habitat, which remains a key research goal (Hardy,
1996).
Temporal variations in the use of physical habitat
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391
Physical habitat assessment 387
can be examined from the short-term (e.g. diurnal
shifts in fish habitat requirements, or differences
required for activities such as spawning and feeding
(Shirvell & Dungey, 1983)), to the long-term (e.g.
examining possible limiting events such as droughts
within a flow series to identify the habitat `bottle-
necks' restricting the age structure of the resident
community (Garcia de Jalon, 1995)). PHABSIM stu-
dies (e.g. Petts & Maddock, 1994; Johnson, Elliott &
Gustard, 1995) have commonly combined a flow time
series with a habitat vs. discharge relationship to
produce a habitat time series and habitat duration
curve (Fig. 5). However, the effects of limiting events
of different durations has not been accurately identi-
fied. For example, we cannot accurately indicate the
effects of a given limiting event for two days,
compared with five days, 10 days or 1 month.
It is clear that there are some important research
goals relating to the spatial and temporal aspects of
physical habitat assessment. Future research on the
development of physical habitat assessment methods
should strive to incorporate and integrate the range of
spatial and temporal scales that are apparent in
determining the health of streams.
Acknowledgements
The author thanks the CRC for Freshwater Ecology at
the University of Canberra for their invitation and
financial support to attend and present this paper at
the `What Is River Health?' conference. Thanks also to
the anonymous referees for their constructive com-
ments on an earlier draft.
References
Aadland L.P. (1993) Stream habitat types: their fish
assemblages and relationship to flow. North American
Journal of Fisheries Management, 13, 790±806.
Amoros C., Roux A.L. & Reygrobellet J.L. (1987) A
method for applied ecological studies of fluvial
hydrosystems. Regulated Rivers: Research and Manage-
ment, 1, 17±36.
Barmuta L.A. (1989) Habitat patchiness and macro-
benthic community structure in an upland stream in
temperate Victoria, Australia. Freshwater Biology, 21,
223±236.
Bartsch N., Gubala C.P. & Hardy T.B. (1996) Determining
habitat criteria for the endangered fountain darter
through aquatic mapping and hydrologic modeling.
388 I. Maddock
Proceedings of the 2nd International Symposium on
Habitats and Hydraulics, Vol. B (Eds M. Leclerc, H.
Capra, S. Valentin, A. Boudreault and I. Cote), pp. 251±
262. Quebec City, Canada.
Binns N.A. & Eiserman F.M. (1979) Quantification of
fluvial trout habitat. Transactions of the American Fish-
eries Society, 108, 215±228.
Bisson P.A., Nielsen J.L., Palmason R.A. & Grove L.E.
(1982) A system of naming habitat types in small
streams, with examples of habitat utilisation by
salmonids during low stream flow. Acquisition and
Utilisation of Aquatic Habitat Information (Ed. N.B.
Armandtrout), pp. 62±73. Western Division of the
American Fisheries Society, Portland, OR.
Bisson P.A., Sullivan K. & Nielsen J.L. (1988) Channel
hydraulics, habitat use and body form of juvenile coho
salmon, steelhead, and cutthroat trout in streams.
Transactions of the American Fisheries Society, 117, 262±
273.
Boon P.J. (1992) Essential elements in the case for river
conservation. River Conservation and Management (Eds
P.J. Boon, P. Calow and G.E. Petts), pp. 11±33. Wiley,
Chichester.
Bovee K.D. (1982). A guide to stream habitat analysis using
the Instream Flow Incremental Methodology. Instream
Flow Information Paper no. 12. FWS/OBS-82±26, US
Fish and Wildlife Service Biological Services Program,
Cooperative Instream Flow Service Group.
Bovee K.D. (1996) Perspectives on two-dimensional river
habitat models: the PHABSIM experience. Proceedings
of the 2nd International Symposium on Habitats and
Hydraulics, Vol. B (Eds M. Leclerc, H. Capra, S.
Valentin, A. Boudreault and I. Cote), pp. 149±162.
Quebec, Canada.
Bowlby J.N. & Roff J.N. (1986) Trout biomass and habitat
relationships in Southern Ontario streams. Transactions
of the American Fisheries Society, 115, 503±514.
Brooker M.P. (1981) The impact of impoundments on the
downstream fisheries and general ecology of rivers.
Advances in Applied Ecology, Vol. 6 (Ed. T.H. Coaker),
pp. 91±152. Academic Press, New York.
Brookes A. (1988) Channelized Rivers: Perspectives for
Environmental Management. Wiley, Chichester.
Brookes A. & Shields F.D. Jr, (Eds) (1996) River Channel
Restoration: Guiding Principles for Sustainable Projects.
Wiley, Chichester.
Calow P. & Petts G.E., eds. (1994). The Rivers Handbook,
Vol. 2. Blackwell Scientific, Oxford.
Cornelius S.C., Sear D.A., Carver S.J. & Heywood D.I.
(1994) GPS, GIS and geomorphological field work.
Earth Surface Processes and Landforms, 19, 777±787.
Downs P.W. & Brookes A. (1994) Developing a standard
geomorphological approach for the appraisal of river
projects. Integrated River Basin Development (Eds C.
Kirby and W.R. White), pp. 299±310. Wiley, Chichester.
Fausch K.D. & White R.J. (1981) Competition between
brook trout (Salvelinus fontinalis) and brown trout
(Salmo trutta) for positions in a Michigan stream.
Canadian Journal of Fisheries and Aquatic Sciences, 38,
1220±1227.
Fix R.E. & Burt T.P. (1995) Global Positioning System: an
effective way to map a small area or catchment. Earth
Surface Processes and Landforms, 20, 817±827.
Fox P.J.A., Naura M. & Raven P. (1996) Predicting habitat
components for semi-natural rivers in the United
Kingdom. Proceedings of the 2nd International Symposium
on Habitats and Hydraulics, Vol. B (Eds M. Leclerc, H.
Capra, S. Valentin, A. Boudreault, and I. Cote), pp.
227±237. Quebec, Canada.
Frissell C.A., Liss W.J., Warren C.E. & Hurley M.D.
(1986) A hierarchical framework for stream habitat
classification: viewing streams in a watershed context.
Environmental Management, 10, 199±214.
Garcia de Jalon D. (1995) Management of physical habitat
for fish stocks. The Ecological Basis for River Management
(Eds D. Harper and P. Barham), pp. 363±374. Wiley,
Chichester.
Gilbert C. (1993) Portable GPS systems for mapping:
features versus benefits. Earth Observation Magazine,
(October), 43±48.
Glova G. & Duncan M.J. (1985) Potential effects of
reduced flows on fish habitats in a large braided river,
New Zealand. Transactions of the American Fisheries
Society, 114, 165±181.
Gubala C.P., Branch C., Roundy N. & Landers D. (1994)
Automated global positioning system charting of
environmental attributes: a limnologic case study.
Science of the Total Environment, 148, 83±92.
Gubala C.P., Eilers J.M. & Bernert J.A. (1996) The
relationships between river channel morphometry,
complexity and aquatic habitat. Proceedings of the 2nd
International Symposium on Habitats and Hydraulics, Vol.
B (Eds M. Leclerc, H. Capra, S. Valentin, A. Boudreault,
and I. Cote), pp. 299±306. Quebec, Canada.
Habersack H. & Nachtnebel H.P. (1995) Short-term
effects of local river restoration on morphology, flow
field, substrate and biota. Regulated Rivers: Research and
Management, 10, 291±301.
Hardy T.B. (1996) The future of habitat modeling.
Proceedings of the 2nd International Symposium on
Habitats and Hydraulics, Vol. B (Eds M. Leclerc, H.
Capra, S. Valentin, A. Boudreault, and I. Cote), pp.
447±461. Quebec, Canada.
Harper D.M., Smith C.D. & Barham P.J. (1992) Habitats
as the building blocks for river conservation assess-
ment. River Conservation and Management (Eds P.J.
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391

Boon, P. Calow and G.E. Petts), pp. 311±319. Wiley,
Chichester.
Harper D., Smith C., Barham P. & Howell R. (1995) The
ecological basis for the management of the natural
river environment. The Ecological Basis for River Manage-
ment. (Eds D.M. Harper, and A.J.D. Ferguson), pp. 219±
238. Wiley, Chichester.
Hill J. & Grossman G.D. (1993) An energetic model of
microhabitat use for rainbow trout and rosyside dace.
Ecology, 74, 685±698.
Hvidsten N.A. & Johnsen B.O. (1992) River bed construc-
tion: impact and habitat restoration for juvenile Atlantic
Salmon, Salmo salar L. & brown trout, Salmo trutta L.
Aquaculture and Fisheries Management, 23, 489±498.
Hynes H.B.N. (1968) Further studies on the invertebrate
fauna of a Welsh mountain stream. Archives Hydro-
biologia, 65, 360±379.
Johnson I.W., Elliott C.R.N. & Gustard A. (1995)
Modelling the effect of groundwater abstraction on
salmonid habitat availability in the River Allen, Dorset,
England. Regulated Rivers: Research and Management, 10,
229±238.
Jordan W.R., Gilpin M.E. & Aber J.D., (Eds) (1987)
Restoration Ecology. Cambridge University Press, Cam-
bridge.
Jowett I.G. (1993) A method for objectively identifying
pool, run, and riffle habitats from physical measure-
ments. New Zealand Journal of Marine and Freshwater
Research, 27, 241±248.
Jowett I.G. (1997) Instream flow methods: a comparison
of approaches. Regulated Rivers: Research and Manage-
ment, 13, 115±127.
Karr J.R. (1981) Assessment of biotic integrity using fish
communities. Fisheries, 6, 21±26.
Kershner J.L. & Snider W.M. (1992) Importance of a
habitat-level classification system to design instream
flow studies. River Conservation and Management (Eds
P.J. Boon, P. Calow and G.E. Petts), pp. 179±193. Wiley,
Chichester.
Ladson A.R., White L.J., Doolan J.A., Finlayson B.L., Hart
B.T., Lake P.S. & Tilleard J.W. (1998) Development and
testing of an Index of Stream Condition for waterway
management in Australia. Freshwater Biology, 41, 453±
468.
Lewis S.L. (1969) Physical factors influencing fish
populations in pools of a trout stream. Transactions of
the American Fisheries Society, 948, 14±19.
Maddock I.P. & Bird D. (1996) The application of habitat
mapping to identify representative PHABSIM sites on
the River Tavy, Devon, UK. Proceedings of the 2nd
International Symposium on Habitats and Hydraulics, Vol.
B (Eds M. Leclerc, H. Capra, S. Valentin, A. Boudreault
and I. Cote), pp. 203±214. Quebec, Canada.
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391
Physical habitat assessment 389
Maddock I.P., Petts G.E. & Bickerton M.A. (1995) River
channel assessment ± a method for defining channel
sectors on the River Glen, Lincolnshire, UK. Man's
Influence on Freshwater Ecosystems and Water Use (Ed.
G.E. Petts), pp. 219±226. Proceedings of the IAHS
Conference, Boulder, CO, July 1995. IAHS Publication
no. 230, Wallingford.
McClendon D.D. & Rabeni C.F. (1987) Physical and
biological variables useful for predicting population
characteristics of smallmouth bass and rock bass in an
Ozark stream. North American Journal of Fisheries
Management, 7, 46±56.
Meffe G.K. & Sheldon A.L. (1988) The influence of
habitat structure on fish assemblage composition in
southeastern blackwater streams. American Midland
Naturalist, 120, 225±240.
Milhous R.T., Wegner D.L. & Waddle T. (1984)
Users guide to the Physical Habitat Simulation System
(PHABSIM). Instream Flow Information Paper no. 11.
U.S. Fish and Wildlife Service, FWS/OBS-81/13 (re-
vised).
Miller J.R. & Ritter J.B. (1996) An examination of the
Rosgen classification of natural rivers. Catena, 27, 295±
299.
Milner N.J., Hemsworth R.J. & Jones B.E. (1985) Habitat
evaluation as a fisheries management tool. Journal of
Fish Biology, 27 (Suppl. A), 85±108.
Modde T., Ford R.C. & Parsons M.G. (1991) Use of
habitat-based stream classification system for categor-
ising trout biomass. North American Journal of Fisheries
Management, 11, 305±311.
Muhar S. (1996) Habitat improvement of Austrian rivers
with regard to different scales. Regulated Rivers:
Research and Management, 12, 471±482.
Naiman R.J., Lonzarich D.G., Beechie T.J. & Ralph S.C.
(1992) General principles of classification and the
assessment of conservation potential in rivers. River
Conservation and Management (Eds P.J. Boon, P. Calow
and G.E. Petts), pp. 93±123. Wiley, Chichester.
Nestler J., Milhous R.T. & Layzer J.B. (1989) Instream
habitat modeling techniques. Alternatives in Regulated
River Management (Eds J.A. Gore and G.E. Petts), pp.
295±316. CRC Press, Boca Raton, FL.
Newbury R.W. (1984) Hydrologic determinants of aqua-
tic insect habitats. The Ecology of Aquatic Insects (Eds
V.H. Resh and D.M. Rosenberg), pp. 323±357. Praeger,
New York.
Nowell A.R.M. & Jumars P.A. (1984) Flow environments
of aquatic benthos. Annual Review of Ecology Systema-
tics, 15, 303±328.
NRA (1996) River Habitats in England and Wales: a National
Overview. River Habitat Survey Report no. 1. National
Rivers Authority, Bristol.
390 I. Maddock
O'Neill M.P. & Abrahams A.D. (1984) Objective identi-
fication of pools and riffles. Water Resources Research,
20, 921±926.
Ohio EPA (1987) Biological Criteria for the Protection of
Aquatic Life, Vol. I. The Role of Biological Data in Water
Quality Assessment. Division of Water Quality Monitor-
ing and Assessment, Surface Water Section, Ohio
Environmental Protection Agency, Columbus, Ohio.
Panja K. & Hardy T.B. (1995) Comparison of multi-
spectral videography based classification of mesoscale
habitats and ground based mapping under turbid
riverine conditions. Proceedings of the 15th Workshop on
Color Photography and Videography for Resource Assess-
ment. Indiana State University, Indiana, May 2±3,
1995.
Parasiewicz P. (1996) Estimation of physical habitat
characteristics using automation and geodesic-based
sampling. Regulated Rivers: Research and Management,
12, 575±583.
Petts G.E. (1984) Impounded Rivers. Wiley, Chichester.
Petts G.E. (1994) Rivers: dynamic components of catch-
ment ecosystems. The Rivers Handbook, Vol. 2 (Eds P.
Calow and G.E. Petts), pp. 3±22. Blackwell Scientific,
Oxford.
Petts G.E. & Maddock I.P. (1994) Flow allocation for in-
river needs. The Rivers Handbook, Vol. 2 (Eds P. Calow
and G.E. Petts), pp. 289±307. Blackwell Scientific,
Oxford.
Petts G.E., Maddock I.P., Bickerton M.A. & Ferguson A.
(1995) Linking hydrology and ecology: the scientific
basis for river management. The Ecological Basis for
River Management (Eds D. Harper and P. Barham), pp.
1±16. Wiley, Chichester.
Plafkin J.L., Barbour M.T., Porter K.D., Gross S.K. &
Hughes R.M. (1989) Rapid Bioassessment Protocols for
Use in Streams and Rivers: Benthic Macroinvertebrates and
Fish. United States Environmental Protection Agency,
EPA/444/4±89±001, Washington DC.
Poff N.L. & Ward J.V. (1989) Implications of streamflow
variability and predictability for lotic community
structure: a regional analysis of streamflow patterns.
Canadian Journal of Aquatic Sciences, 46, 1805±1818.
Rabeni C.F. & Jacobson R.B. (1993) The importance of
fluvial hydraulics to fish-habitat restoration in a low
gradient alluvial stream. Freshwater Biology, 29, 211±
220.
Richards K.S. (1976) The morphology of riffle-pool
sequences. Earth Surface Processes and Landforms, 1,
71±88.
Richter B.D., Baumgartner J.V., Powell J. & Braun D.P.
(1996) A method for assessing hydrologic alteration
within ecosystems. Conservation Biology, 10, 1163±1174.
Rosenberg D.M. & Resh V.H., eds. (1993) Freshwater
Biomonitoring and Benthic Macroinvertebrates. Chapman
& Hall., London.
Rosgen D.L. (1985) A Stream Classification System. USDA
Forest Service General Technical Report, RM 120.
Rosgen D.L. (1994) A classification of natural rivers.
Catena, 22, 169±199.
Rosgen D.L. (1996) Applied River Morphology. Wildland
Hydrology, Pagosa Springs, CO.
RRP (1993) Phase I Feasibility Study: Final Report. The
River Restoration Project, Huntingdon, UK.
Scullion J., Parish C.A., Morgan N. & Edwards R.W.
(1982) Comparison of benthic macroinvertebrate fauna
and substratum composition in riffles and pools in the
impounded River Elan and the unregulated River Wye,
mid-Wales. Freshwater Biology, 12, 579±595.
Shirvell C.S. & Dungey R.G. (1983) Microhabitats chosen
by brown trout for feeding and spawning in rivers.
Transactions of the American Fisheries Society, 112, 355±
367.
Simonson T.D., Lyons J. & Kanehl P.D. (1994) Quantify-
ing fish habitat in streams: transect spacing, sample
size, and a proposed framework. North American
Journal of Fisheries Management, 14, 607±615.
Southall P.D. & Hubert W.A. (1984) Habitat use by adult
paddlefish in the upper Mississippi River. Transactions
of the American Fisheries Society, 113, 125±131.
Stafford J.V., Le Bars J.M. & Ambler B. (1996) A hand-
held data logger with integral GPS for producing weed
maps by field walking. Computers and Electronics in
Agriculture, 14, 235±247.
Stalnaker C. (1979) The use of habitat structure prefer-
enda for establishing flow regimes necessary for
maintenance of fish habitat. The Ecology of Regulated
Streams (Eds J.V. Ward & J.A. Stanford). Plenum Press,
London.
Stalnaker C., Lamb B.L., Henriksen J., Bovee K. &
Bartholow J. (1994) The Instream Flow Incremental
Methodology: a Primer for IFIM. National Ecology
Research Center, Internal Publication. National Biolo-
gical Survey, Fort Collins, CO.
Swales S. (1989) The use of instream habitat improve-
ment methodology in mitigating the adverse effects of
river regulation on fisheries. Alternatives in Regulated
River Management (Eds J.A. Gore and G.E. Petts), pp.
185±208. CRC Press, Boca Raton, FL.
Sweeting R.A. (1994) River Pollution. The Rivers Hand-
book, Vol. 2 (Eds P. Calow and G.E. Petts), pp. 23±32.
Blackwell Scientific, Oxford.
The Surface Water Regulations (1994) Surface Waters
(River Ecosystem) (Classification) Regulations. SI, 1994
(1057), UK.
Thorne C.R. & Easton K. (1994) Geomorphological
reconnaissance of the River Sence, Leicestershire
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391

for river restoration. East Midland Geographer, 17, 40±
50.
Van Sickle J. (1996) GPS for Land Surveyors. Ann Arbor
Press, Michigan.
Van Winkle W., Rovse K.A. & Chambers R.C. (1993)
Individual-based approach to fish population dy-
namics: an overview. Transactions of the American
Fisheries Society, 122, 397±403.
ã 1999 Blackwell Science Ltd, Freshwater Biology, 41, 373±391
Physical habitat assessment 391
Ward J.V. & Stanford J.A.,. eds. (1979). The Ecology of
Regulated Streams. Plenum Press, London.
Western A.W., Finlayson B.L., McMahon T.A. & O'Neill
I.C. (1997) A method for characterising longitudinal
irregularity in river channels. Geomorphology, 21, 39±51.
(Manuscript accepted September 1998)