Biological Report 29
March 1995

The Instream Flow Incremental
Methodology
A Primer for IFIM•

National Biological Service

U.S. Department of the Interior

Biological Report 29
March 1995

The Instream Flow Incremental Methodology
A Primer for IFIM
byClair Stalnaker
Berton L. LambJim Henriksen
Ken Bovee
John Bartholow

U.S. Department of the Interior
National Biological Service
Washington, D.C. 20240

Preface
This booklet is a primer on the Instream Flow Incremental Methodology (IFIM). Our objective forthis primer is to give you a short but comprehensive introduction to the background, philosophical andecological underpinnings, individual components, and steps in applying IFIM. As a primer, we have
tried to keep it simple. Scientific names and other technical details have been avoided, but the primer
includes relevant definitions (with key words or phrases indicated in italics for their first use),summaries of the literature where you may wish to turn for further reading, and explanations to increase
your understanding of what IFIM is all about and how it works. The primer should reinforce yourgrowing knowledge and provide the necessary stepping stones into more advanced, certified training in
IFIM methods.
This primer is divided into five more or less independent sections. The first section reviews the history
of instream flow problems in the United States. Reading this section should provide you with anunderstanding of why IFIM emerged to solve certain complex water management problems and hint at
future directions. The second section discusses the choice of instream flow methods and, more
importantly, provides a framework for deciding whether IFIM is appropriate for the kind of problems
you might be facing. The third section reviews the ecological underpinnings of IFIM from a historicalperspective. This section is meant to show you the degree to which IFIM components, or models,represent the essence of the biological systems that we are attempting to understand. It is more detailed
than the other sections and meant specifically to be of interest to biologists and ecologists. Section fourdelves into the broader philosophical, problem-solving approach embodied in IFIM. This perspective isimportant because the 'facts' alone rarely dictate good decisions; it is how we employ those facts toresolve instream flow problems in an interdisciplinary decision making arena that is important. The
fifth section outlines the logical steps in applying IFIM and the information flow that holds them
together. Here you will learn how to navigate through the IFIM process from tentative problem
identification to problem resolution.
Our objectives for this primer do not stop at the last page. We hope that as you learn more about
IFIM, you may be motivated to continue your learning by enrolling in one or more of several advanced
courses dealing with IFIM. Please contact Conference Services at Colorado State University, Fort
Collins, Colorado 80523, or call 303-491-7767 for more course information and a catalog of available
National Biological Service courses sponsored by CSU. Technical questions should be directed to ouroffice at the address below.
We encourage IFIM users to suggest improvements that may increase the utility and effectivenessof our products. Please use the comment form at the back of this booklet or send suggestions to:
Midcontinent Ecological Science Center
National Biological Service
4512 McMurry Avenue
Fort Collins, Colorado 80525-3400
303-226-9332
FAX 303-226-9230
e-mail: Stalnakere@mail.nbs.gov

Contents
Preface ............................................................................................................................................... iii
Chapter 1. The History of Instream Flow Problems and IFIM .................................................. 2
Minimum Flow Standards Provide Minimal Protection ............................................................. 2
Impact Analyses Lead to Increased Resource Protection .......................................................... 2
Water Budgets Establish Fisheries as a Legitimate Management Purpose ............................. 3
Multiple Use Implies Interdisciplinary Analyses ......................................................................... 4
Development of IFIM ...................................................................................................... 4
Extending IFIM Into the Future ................................................................................................ 6
Chapter 2. Choosing the Appropriate Assessment Tools ................................................................ 8
A Dichotomy of Techniques ......................................................................................................... 8Standard-Setting Techniques ...................................................................................................... 9
Hydrologic Records ................................................................................................................. 10
The Tennant Method ............................................................................................................... 10
Mid-Range Techniques: A Little More Than Basic Standard-Setting But Not Quite

Incrementalism ......................................................................................................... 11
Modified Tennant Approach ................................................................................................... 11
Wetted Perimeter Technique ................................................................................................... 11
Multiple Attribute Standard-Setting Methods ......................................................................... 12
Incremental Techniques .............................................................................................................. 13
Conclusion ................................................................................................................................... 15
Chapter 3. Ecological Underpinnings of IFIM ......................................................................... 16
Longitudinal Succession ............................................................................................................... 16
Habitat Segregation .................................................................................................................... 16
Reproductive Success ............................................................................................................... 17
Energetics ................................................................................................................................ 18
Habitat Bottlenecks .................................................................................................................. 19
Conclusion ................................................................................................................................... 20
Chapter 4. Philosophical Underpinnings of IFIM .................................................................... 22
Axioms ......................................................................................................................................... 22
Approach ...................................................................................................................................... 23
Flow Regime ............................................................................................................................. 24
Habitat Structure .................................................................................................................... 24
Water Quality .......................................................................................................................... 24
Food Energy Source ................................................................................................................. 26
Biotic Interactions .................................................................................................................... 26
Stream Habitat as an Integrator of Man's Influence on Stream Systems ............................. 26
Chapter 5. The Application of IFIM ...................................................................................... 28
Problem Identification ................................................................................................................. 28
Study Planning ............................................................................................................................. 28
Study Implementation ................................................................................................................. 29

PHABSIM ................................................................................................................... 30................................................................................................................. 32

Alternatives Analysis

VProblem Resolution ......................................................................................................... 32
For More Information ...................................................................................................... 33
Cited Literature ................................................................................................................... 33
Glossary .............................................................................................................................. 39
Reader Comment Form for Primer ......................................................................................... 45

FiguresFig. 1.1. Overview of the Instream Flow Incremental Methodology ............................................. 5
Fig. 2.1. Use of the wetted perimeter method to estimate instream flows. .................................. 12
Fig. 2.2. Flow-habitat relation developed by using PHABSIM
13
Fig. 2.3. Suitability-of-use curves for brown trout. ................................................................. 13
Fig. 2.4. Example fish population size related to usable habitat area using the IFIM
14
Fig. 2.5. Duration analysis of habitat available under baseline conditions,with-project, and after mitigation of project .......................................................................... 15
Fig. 2.6. Spectrum of problem-solving methodologies. ............................................................ 15
Fig. 3.1. Longitudinal succession schematic. Shading denotes approximate gradientfrom headwaters to intermediate stream to mature river. .................................................... 17
Fig. 3.2. An example of microhabitat specificity. .................................................................... 17
Fig. 4.1. Species periodicity chart. ......................................................................................... 24
Fig. 4.2. Channel aggradation'compared with degradation. .................................................... 26
Fig. 5.1. Calibration process .................................................................................................... 30
30
Fig. 5.2. Total habitat combines elements of macrohabitat and microhabitat.
Fig. 5.3 Conceptualization of how PHABSIM calculates habitat values as a functionof discharge. ................................................................................................................... 31

TablesTable 2.1. The opposite ends of the problem-solving spectrum .................................................. 9
Table 2.2. Instream flow analysis based on the Tennant method ............................................ 11
Table 4.1. Major factors influencing habitat of river ecosystems based on spatial scaleof the processes ................................................................................................................. 23
Table 4.2. Primary ways that human-induced alterations impact river ecosystem
biological integrity ........................................................................................................... 25
Table 4.3. IFIM models developed for integrating the spatial and temporal scales ofhabitat analyses .............................................................................................................. 27vi

2

BIOLOGICAL REPORT 29

Chapter 1. The History of Instream
Flow Problems and IFIM

Instream flow methods have been developed predominantly by biologists and hydrologists working
for agencies having regulatory responsibility related to water development and management (Stalnaker and Arnette 1976). Such efforts over the last
30 years have provided the impetus for detailed
ecological studies leading to a significant growth in
the understanding of the relations between stream
flow and aquatic habitats. Most of the empiricalevidence gathered to date has focused on fish andbenthic macro-invertebrate habitat requirements,
with recent emphasis on the relation between
stream flow and woody riparian vegetation andriver-based recreation (Gore 1987; Orth 1987;
Brown 1992; Shelby et al. 1992; Scott et al. 1993).
Water management problem solving has matured
from setting fixed minimum flows with no specificaquatic habitat benefit to incremental methods inwhich aquatic habitats are quantified as a functionof stream discharge. Within this historical progression we also saw the application of a water budget
which set the stage for having the fisheries manager be an integral part of an interdisciplinary
decision-making system. This chapter will review
the progression of circumstances and techniquesleading to the development of IFIM and point toward what the future might hold.

Minimum Flow Standards
Provide Minimal Protection
Following the large reservoir and water development era of the mid-twentieth century in North
America, resource agencies became concerned overthe loss of many miles of riverine fish and wildlife
resources in the arid western United States. Consequently, several western states began issuingrules for protecting existing stream resources fromfuture depletions caused by accelerated water development. Many assessment methods appeared
during the 1960's and early 1970's. These techniques were based on hydrologic analysis of
the water supply and hydraulic considerations ofcritical stream channel segments, coupled with
empirical observations of habitat quality and anunderstanding of riverine fish ecology, most notably the Pacific salmon and freshwater trouts. Collectively, the efforts led to a general class of instream flow assessment techniques (models)meant to help reserve a specific amount of water
within the channel for the benefit of fish and otheraquatic life (Wesche and Rechard 1980; Morhardt
1986; Stalnaker 1993). Application of these methods usually resulted in a single threshold or 'minimum' flow value for a specified stream reach below
which water may not be withdrawn for consumptive water use. The minimum flow is almost always less than the optimal or pristine habitat
condition, yet these 'reservations' of water form thecurrent basis for issuing water permits in manystates. See MacDonnell et al. (1989) and Lamb andLord (1992) for recent discussions of the status ofstate recognition and protection of flowing water
for instream flow.

Impact Analyses Lead toIncreased Resource Protection
Following enactment of the National Environmental Policy Act (NEPA) of 1970, attention was
shifted from minimum flows to the evaluation ofalternative designs and operations of federally
funded water projects. Methods capable of quantifying the effect of incremental changes in streamflow to evaluate a series of possible alternative
development schemes were needed (Stalnaker
1993). This need led to the development of habitat
versus discharge functions developed from lifestage-specific relations for selected species, that is,fish passage, spawning, and rearing habitat versus
flow for trout or salmon. Corroborating research
took the form of analyses correlating the general
well-being of fish populations (usually in terms of
measured standing crop) with various physical andchemical attributes of the stream flow regime andits interaction with the stream channel structure

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 3(Binns and Eiserman 1979). A set of these variablesconsistently was shown to contribute significantly
to the variation in fish population and production.
These variables were water velocity, minimal
water depths, instream objects such as cover, bottom substrate materials (with particular emphasison the amount of fines in the interstitial spaces
within coarse bed elements), water temperature,
dissolved oxygen, total alkalinity, turbidity, andlight penetration through the water column (Gosseand Helm 1981; Shirvell and Dungey 1983). Thesevariables were integrated into methodologies foranalyzing the consequences of proposed water
withdrawal or storage-release activities and wereapplied to many federal water projects operated by
the Bureau of Reclamation, Army Corps of Engineers, and Tennessee Valley Authority (Nestler
et al. 1989).
During the late 1970's and early 1980's, an eraof small hydropower development began. Hundredsof proposed hydropower sites in the Pacific Northwest and New England regions of the United Statescame under intensive examination by state andfederal fishery management interests. During thistransition period from evaluating large federal reservoirs to evaluating license applications for smallhydropower, the Instream Flow Incremental Methodology (IFIM) was developed under the guidanceof the U.S. Fish and Wildlife Service (Trihey and
Stalnaker 1985). This methodology attempted tointegrate the planning concepts of water supply,
analytical models from hydraulic and water quality
engineering, and empirically derived habitat versus flow functions. This methodology produced
simulations of the quantity and quality of 'potential habitat' resulting from proposed water development, illustrated through a series of alternative
flow regimes. Such efforts involving incremental
methods and analyses of alternatives through time
were further enhanced during the next 10 years,
driven by several hundred relicensing applications
submitted to the Federal Energy Regulatory Commission. Most of these applications involved reservoirs that had been in place for 30-50 years without
any downstream instream flow considerations factored into their operating procedures.
Opportunities were seen by the natural resource
agencies to restore riverine aquatic resources that
had been impacted (occasionally eliminated) for
many decades. Conversely, many hydropower companies wanted to shift their operating protocol toward hydropeaking and pump-storage to enhance
the revenues at existing installations. Many ofthese peaking projects operated by private powercompanies or public utilities were readily accessible
for recreational use. The recreational interests
seized on the relicensing opportunity as a means toenhance river recreational use by canoes, kayaks,
and rafts. NEPA guidelines for examining alternatives and hydropower relicensing forced UnitedStates decision makers to balance potential conflicts among users of the riverine resources. Incremental methods became the tools of choice for quantitatively describing the consequences ofalternative ways of managing flowing waters, setting the stage for negotiation among various interest groups and better informing the decision makers in their role in conflict resolution (Stalnaker
1993).

Water Budgets Establish
Fisheries as a Legitimate
Management Purpose
As the multiple-use ethic emerged over the lasttwo decades, it became clear that simply allocating
part of the water supply to various uses is not
sufficient to resolve conflicts. The same water canbe used many times if it is managed so that thetiming of release serves instream purposes whilestill being delivered to downstream consumptive
users. This multiple-use management philosophy,
exemplified by the Pacific Northwest ElectricPower Planning and Conservation Act of 1980 and
subsequent efforts by the Bonneville Power
Authority, allowed federal, state, and tribal fisherybiologists to identify management prescriptions forrestoration and enhancement of the anadromous
salmon runs in the Columbia River basin. A minimum flow did not provide sufficient protection for
stream resources during drought cycles, nor did it
provide the opportunity for optimal fish production
during wet years. Water budgets allocating a portion of water stored in upstream reservoirs forfishery benefits reserve flows that could be released
when they were most needed (Waddle 1991). When
downstream water users are not calling for delivery
through critical spawning or rearing reaches, the'fish water' can be released to relieve any habitatinduced bottlenecks.
A recent case study by the National ResearchCouncil (1992) recognized the value of reservoir
release management in alleviating conflict and enhancing multiple uses (including instream) withinarid western United States river basins. The

4

RioLoGICAL REPORT 29

Yakima River basin in Washington, focusing on
Pacific salmon restoration, and the Truckee-Carson River systems in Nevada, emphasizing endangered species and terminal wetland habitat recovery, were highlighted as examples of emerging
multiple-use management. Assigning a reservoir
water budget to the fisheries for downstream habitat management is now being seriously consideredduring the operations evaluation phase of manylarge federal water storage projects. The traditional water user groups (for example, irrigatedagriculture, municipal, and industrial) may prefersuch reservoir water budget management because
the fish water is treated the same as other water inthe system, and the call for water must be decided
by the fishery manager, relieving the reservoir
operator and other users in the system from having
to decide how and when the instrearn flows are to
be delivered.
The shift from a set of minimum flow constraints
to a water budget set aside specifically for fisheries
purposes changed the role of the fisheries manager
in river systems in the United States. From now on,
to be most effective, the fishery resource managers
must become water and habitat managers. Thus,
natural resource agencies need to acquire a moreinterdisciplinary mix among their employees.
These contemporary agencies must be prepared todecide about the delivery of water on a daily basis
during particular seasons and to decide what portion of the river basin fishery resource will befavored (and conversely what part sacrificed) during droughts. By adopting water budgets, a mutual'sharing' of storage in federal water projects acrossall user groups during droughts is facilitated. Under the traditional diversionary allocation philosophy of 'first-in-time-first-in-right' practiced under
Western water appropriation doctrine, the fishery
may have first priority during a water-short year
(if flows are reserved by appropriation) or last priority (if allocated a very junior water right). By
gaining a 'seat at the management table' the instream-fishery interests get part of the water
stored during high-flow periods for release whenthe most critical conditions occur downstream.
Sharing the storage allows for delivery to relievethese critical conditions.

Multiple Use Implies
Interdisciplinary Analyses
Multiple-use management of water at the river
basin level is widely recognized as essential in the

United States. A recent study by the National Research Council (1992) points out that managementof reservoirs for single purposes such as irrigationor hydro-electric production is no longer sociallyacceptable. Efficient use of water must incorporatea multitude of instream and consumptive uses
throughout a river basin. This management will
require an interdisciplinary group of professional
water managers to establish procedures for evaluating the water supply, distributing the water, andsharing the consequences of low supply. Resolving
conflicts among states and user groups sharing thesame river system calls for interjurisdictional riverboards or commissions to manage water stored inpublic reservoirs for instream and out-of-stream
uses. Agency resource personnel will be asked toapply state-of-the-art tools, extensively temperedwith judgement and experience, to day-to-day decision making. Fishery and recreation agency managers will make recommendations on seasonal andmonthly bases, dependent on forecasted water supply and available storage. Stream ecologists have asubstantial challenge before them to provide research data to enhance the ability of resource managers to make these decisions. Research is needed
to improve and validate relations between fish,
wildlife, and riparian vegetation and the stream
flow regime. New research is needed for groups oforganisms (guilds) and habitat variables that are
not currently factored into the decisionmaking
process.

Development of IFIM
IFIM unfolded against the backdrop of minimum
flow standards, quantitative impact analyses,
water budgets, and interdisciplinary analyses. The
specific impetus was the National Environmental
Policy Act, which mandated all federal water resource agencies to consider alternative water development and management schemes. This requirement placed increased responsibility on natural
resource agencies for methods, evaluations, andrecommendations related to reservoir storage andrelease and stream channel depletions. IFIM wasdeveloped by an interdisciplinary team and wasfounded on a basic understanding and descriptionof the water supply and habitats within stream
reaches of concern. Historical analysis of the flow
regime using a monthly or weekly tirnestep to describe the reference or baseline hydrologic conditions was considered essential because this type ofanalysis was normal practice within the water re-THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 5

source engineering profession. Looking at streamflow through time (by constructing a hydrologic
time series) allows one to compare the frequency
and duration of wet and dry periods, to examine thedifference between snow-melt and rain-driven systems, and to determine the intensity and durationof short-term events such as cloud bursts and peaking cycles. To influence operating decisions withinlarge-scale water development settings, a tool wasneeded that underscored conflicts and complementary water uses, considered and evaluated eachuser's needs, and was understandable, acceptable,
and easy to use by a broad clientele. Such decision
arenas involve a diversity of disciplines, including
engineers, hydrologists, biologists, recreation planners, lawyers, and political scientists.
The U.S. Fish and Wildlife Service Directorate
requested direct input from other agencies in thedevelopment of this special methodology. Water
resource professionals were assigned to work on
this cooperative effort for periods up to 4 years.
Engineering, water quality modeling, and planning expertise came from the U.S. Bureau of Reclamation, Soil Conservation Service, Army Corpsof Engineers, Environmental Protection Agency,
and university scientists. Expertise in aquatic
ecology, fishery biology, water law, institutionalarrangements, and planning came from stateagencies. The Intergovernmental Personnel Act
provided the vehicle for these assignments fromstate organizations.
This interagency effort led to the conclusion thatan analytical methodology should handle a variety
of instream flow problems, from simple diversions
from the stream channel to complex storage andrelease schemes involving hydropeaking schedules,
pump-storage, and a network of interconnected reservoirs. For such a methodology to be suitable for
evaluating alternatives, it had to be useful in identifying, evaluating, and comparing potential solutions, be capable of being tailored to a specificstream reach, and be expandable such that reach
information could be applied throughout a river
basin. With this general charter, and building on
historical planning practices using stream reachhydrology, IFIM has developed over a period of
15 years into a river network analysis that incorporates fish habitat, recreational opportunity, andwoody vegetation response to alternative water
management schemes (Bartholow and Waddle
1986; Milhous et al. 1989; Auble et al. 1991). Information is presented as a time series of flow andhabitat at selected points within a river system(Milhous et al. 1990). Figure 1.1 illustrates thegeneral information flow within IFIM; we will discuss the various components of IFIM throughout
the remainder of this booklet.
Optimizing for any one use is contrary to thegeneral philosophy of multiple use; efficiency of use
is defined as the greatest return in the number andquantity of uses, with emphasis on simultaneoususe. It is imprudent to use the simple, intermediate
output (for example, flow/habitat or flow/recreation
functions) to argue for a minimum release or flow
standard chosen from the maximum value on a flow
versus habitat graph. The timing of events acrossseasons is critical to the reproductive success andrelative strength of year classes within fish populations. The temporal distribution of strong versus
weak year classes shows the well-being of the fish

Overview of Incremental Methodology(Start)Yes

Needmore worknow

Yes

Feasible
No
Formulatealternatives

trategydesignMicro-habi1at
model
Macro-habitat
model

Total habitat
model

Network habitat
model

Fig. 1.1. Overview of the Instream Flow
Incremental Methodology.

6

BIOLOGICAL REPORT 29

population and, more importantly, determines thenumber of adults available to the fishery on anannual basis. To illustrate this point, we mustcombine the habitat functions and hydrologic timeseries into a quasi population analysis by displaying habitat quality and quantity through time andspace. The IFIM methodology translates the baseline hydrology into a description of the available or
usable habitat present during that historical period. This description is often called the resource
benchmark, from which fishery scientists identify
enhancements and impacts resulting from proposed water delivery schedules.
By examining recent historical conditions (saythe last 5-10 years) using the power of computer
simulation, it is possible to calibrate a systemmodel using historical data such as annual population indices and trend information, creel census
information, computed year-class strength datafrom age and growth studies, or anecdotal information on the general well-being of fish populations in
one year versus another. If the fishery manager canshow that a simulated habitat analysis over a 1020-year historical hydrologic regime agrees withhistorical information on good years versus poor
years in the fishery, much more credence can beplaced in those models for comparing various alternative futures.
IFIM has been designed for river system management by providing an organizational framework
for evaluating and formulating alternative water
management options. It has been built on the philosophical foundation of hydrological analyses to understand the limits of water supply. Analysis offersa description, evaluation, and comparative displayof water use throughout a river system. Emphasis
is placed on the display of usable habitat acrossseveral years to capture the variability in bothwater supply and habitat. Such comparative information enhances negotiations in the planning andmanagement of the riverine resources. Sharing
limited water during drought cycles and the management of timed releases contribute to compatibility between instream and out-of-stream usergroups and allow for rapid recovery of aquatic populations during favorable conditions.
We are often asked to provide cost estimates for
conducting an IFIM study. One might say thatabout 80% of IFIM studies for a single river segment could be conducted within a 12-month timeframe and cost less than $45,000. But "it depends"
is probably the best answer. It depends on
how many variables are included in the various

models, the sampling strategy, the standards for
quality assurance and quality control, the size ofthe river and accessibility of the physical site, theexperience of those performing the work, the number of alternatives to be analyzed, and the numberof times Murphy meddled from start to finish. A
careful scoping is always in order before proceeding.

Extending IFIM Into the
FutureReiser et al. (1989) surveyed IFIM users andfound that the highest priority research needs areto (1) define the relation between flow, habitat,
and fish production; (2) validate and test the relation of habitat measurements to fish production;and (3) develop new methods for determining flow
requirements. Contemporary research (Hagar
et al. 1988; Cheslak and Jacobson 1990; Auble
et al. 1991; EA Engineering, Science and Technology 1991; Nehring and Anderson 1993; Williamson et al. 1993) is broadening the role of IFIM toprovide fisheries management as well as habitat
management capabilities.
The relation between flow, habitat, and fish production is based on work relating the amount andquality of habitat available to the fish population
at critical stages in its life history (Burns 1971;
Mundie and Traber 1983; Morhardt and Mesick1988). In riverine systems the amount and quantityof suitable habitat can be highly variable within
and among years. At any time, the observed population and biomass of fish may be influenced (depressed or stimulated) by many preceding habitat
events. Long-term habitat reductions from reduced
flows may also be important in determining the fish
population and production (Bovee 1988). National
Biological Service scientists are testing models ofthese new concepts on anadromous salrnonid populations in California and resident trout populations
in Colorado (Bartholow and Waddle 1994;
Bartholow et al. 1993).
Goals of contemporary research are (1) development and validation of a dynamic fishery population model, including response to flow-related
limiting events, specifically physical habitat andtemperature; (2) testing of habitat bottleneck hypotheses; (3) development of processes for evaluating water management strategies to achieve
fish population objectives; (4) testing of strategies
for long-term population support including biotic interactions; and (5) improvement to thoseTHE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 7

existing components of the IFIM necessary to provide a smoothly working set of analytical tools forfish population analysis. Such efforts should expand the state of fisheries science and the art ofwater management by clarifying the effects of
population-limiting habitat events and watertemperatures on movement, growth, and mortality rates of fishes and should provide direct feedback between fish populations and reservoir op-

erations with water budgets for fishery management purposes.
Current emphasis in many federal agencies is
on ecosystem planning and management. It is too
early to tell how IFIM techniques may be utilized
in this current push, but if utilized, applications
must be broader in geographic scope and emphasize longer time horizons than have typically been
employed in the past.

8

BIOLOGICAL REPORT 29

Chapter 2. Choosing the Appropriate
Assessment Tools

Every water management decision that includes
instream flow protection offers a unique challenge.
Instream flow decisions may include a federal permit or license, an operating schedule for a water
storage project, a state instream flow water right,
or an element in a state water management plan.
No matter which of these decisions is being addressed, each requires an understanding of several
factors before an appropriate instream flow assessment technique can be chosen.
Several considerations guide the choice of technology for instrearn flow needs assessments, including statutory authority, history of water use,technical orientation, available fiscal resources,
and time allowed to complete studies. In addition,
there is an ongoing debate about the relative scientific merits of competing instream flow assessment technologies (Granholm et at 1985; Mathur
et al. 1985; Estes and Orsborn 1986). All factors
heighten the challenge of selecting the right technology to guide establishment of stream flow protection. When choosing a technology, the analysts'
concentration is often initially directed to thetechnical details of the procedures, such as measurement of stream transects or operation of computer models. However, experienced professional
biologists and engineers responsible for assessments recognize that harder policy questions
must first be answered. Analysts ultimately decide to use a technique as much because it fits thepolitical and environmental problems they face as
because the technology meets scientific standards(Lamb 1986).

A Dichotomy of Techniques
Political and environmental problems can beconveniently divided into two categories dependingon the objectives of the decision process: standardsetting or incremental. In a standard-setting problem, the analyst is called on to recommend an
instream flow requirement to guide generaland, usually, low-intensity decisions setting a limit

below which water cannot be diverted (Trihey and
Stalnaker 1985). This process might be called preliminary planning. An incremental problem refers
to a high-intensity, high-stakes negotiation over a
specific development project. The term incremental
implies the need to answer the following question:
What happens to the variable of interest (e.g.,aquatic habitat, recreation value) when the flowchanges?
Rather than a clear dichotomy, it may be appropriate to picture these two types of decisions on acontinuum, ranging from the setting of noncontroversial standards for overall planning to conflictover establishing incremental differences in flowlevels. No matter where on the continuum a problem falls, there is an additional question: How
many variables are important? The answer to thisquestion may be as simple as saying the problem
is one species of fish or one type of recreation. The
answer may also be expressed as a flow regime
that meets the needs of several decision variables.
For example, a flow regime may be instituted tosatisfy channel and riparian maintenance, fish
habitat, and recreational uses of the water. Although it is most common for incremental problems to present themselves as multi-purpose
questions, it is not uncommon for standard-setting questions to require answers for more than
one decision variable.
Whether a problem falls under the category ofstandard-setting or incremental is not a questionof scientific credibility; defensible scientific analysis is always required because answers to bothtypes of questions must be trustworthy. Moreover,expert judgement is required in both standardsetting and incremental problems. This judgement comes into play in reaching conclusions
based on the technology that is chosen, as well as
in choosing the appropriate method. There is one
other consideration. Standard-setting techniques
are inappropriate for brokered decisions because
brokered decisions require the exploration of alternatives. In other words, the standard that has

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 9

been set is, by definition, essentially non-negotiable. Standard-setting techniques might be appropriate for arbitrated decisions where the analyst feels safe that the standard-setting reflects
the best evidence (or the most equitable position),that is, whenever there is a rebuttable presumption that the analyst is correct. The problem stillarises in the mid-range situations when the analyst is forced to give a quick answer that will
become the subject of negotiation or arbitration.
Different technical solutions are appropriate foreach of the two poles on this continuum. On the one
hand, inexpensive, straightforward, rule-of-thumbsolutions are well-suited to standard-setting tasks.
For these tasks, the considerations are certainty
that the planning objectives will be met and thatthe recommendations will be easily communicatedto policy makers. On the other hand, incremental
problems are likely to require an in-depth knowledge of the flow requirements of fish and wildlife,
recreation, water quality, and other instream uses,
as well as the ability to integrate these concerns
into plans for a specific project.
Much of the debate that surrounds instream
flow technology is not about the approaches mostsuited to these extreme cases but about the best
technology for problems that fall somewhere in
between. In this mid-range, solutions may havelong time-horizons while still leading to identifiable projects. Inevitably, a quick rule-of-thumbmethod will be found inadequate, followed by amore complicated analysis and demands for compromise.
The choice of an instream flow technique for
mid-range cases is further hampered by the needfor low cost and speed in making the first recommendation. That first recommendation precedes aperiod of wrangling over project benefits and thennegotiation of more in-depth studies. Finally,
these discussions conclude with an expensive
technical analysis and hard bargaining over the
professional judgements of those making andchallenging the never-quite-final recommendations. Other situations can be found or imaginedthat would also fill this middle ground between
long-range planning and specific project negotiations. The choice of initial and follow-up technologies in these types of disputes is a balancing act.
The first simple technology chosen will belinked through the study design to the final project negotiation. How well this linkage can beachieved depends on several factors, including
statutory authority, fiscal resources, training of

Table 2.1. The opposite ends of the problemsolving spectrum.
Standard-setting

Incremental

Low controversy project High controversy project
Reconnaissance-level
Project-specificplanning
Few decision variables Many decision variables
Inexpensive
Expensive
Fast
Lengthy
Rule-of-thumb
In-depth knowledge requiredLess scientificallyMore scientifically accepted
accepted
Not well-suited for
Designed for bargaining
bargaining
Based on historical
Based on fish or habitatwater supply

personnel, and management support for the investigations. Most of all, success in moving fromplanning studies to hard bargaining depends onwhether the analysts guessed correctly about
what would happen to their first recommendations (Olive and Lamb 1984). The range of instream flow assessment techniques can be illustrated both with a summary of these ideas in
Table 2.1 and with the example that follows.

Standard-Setting Techniques
Several techniques are available for the longrange planning of instream flows for fisheries. Ina low-intensity situation, not much detail is required because the questions are straightforward.
Thus, a quick, reconnaissance-level, office-type
approach may be used.
Most standard-setting occurs in statutory state
instream flow protection programs (Lamb andDoerksen 1990). As one analyst observed, "[inmost statutes, it is difficult to either ascertain
legislative intent or determine if a proposed instream flow regime would satisfy the legislative
purpose" (Beecher 1990). An instream flow standard should include the following elements(Beecher 1990): (1) the goal (such as non-degradation), (2) resources (such as fish species), (3) unitof measurement (such as flows in cubic feet per
second left] or habitat in weighted usable area
FWUAD, (4) benchmark period (such as a 10-year
period of record), and (5) protection statistic (suchas the median habitat value for July).

10

BIOLOGICAL REPORT 29

Hydrologic Records
Of the many techniques available for standardsetting related to fisheries, the easiest to use
requires data on the hydrologic records of a
stream. The use of stream gage records assumes
that measured flows support aquatic resources at
acceptable levels (Wesche and Rechard 1980).
This assumption only applies where streams are
essentially undeveloped or where the pattern ofdevelopment has been stable for a long period.
Eastern states increasingly face planning problems associated with undeveloped streams,
whereas most western states have streams already encumbered with sophisticated development projects. In situations where stream flow isdepleted or regulated, the natural flow regime canbe reconstructed from gage records to account forwater diversions and stream modifications (an art
discussed by Bayha (1978); see also other standard techniques in Riggs (1968)). This approach issatisfactory only if the analyst has information on,
or is willing to make assumptions about, the condition of the fishery before development.
Even when pre-development data are available, it is difficult to predict future impacts on theaquatic resources. On some developed streams,
channel structure and fish populations have adjusted to the new flow regime. Existing water
developments may have dampened chronic low- or
high-flow events, thus enhancing the fishery. Developing a knowledge of post-project conditions
will require field investigations. In any case, selecting flows from historical records in the presence of existing development is a limited longrange planning technique.
Where it is possible to use historical records,
several questions arise, for example: Is it best to
recommend a flow based on natural or alteredconditions? What percentage of the historicalstream flow should be recommended? One solution is to use the `aquatic base flow' (Larson 1981;
Kulik 1990). This technique selects the medianflow for the lowest flow month (typically Augustor September) as adequate throughout the year,
unless additional flow releases are required tomeet the needs for spawning and incubation. Another planning scheme involves the use of medianmonthly flows (Bovee 1982). This monthly flowlevel is a surrogate for the natural annual patternof stream flows because it provides a flow thattypifies historical flows for each month.
A hydrologic technique that is inappropriate forestablishing instream flows for fish is the 7-day-

10-year low flow (expressed as 7Q10). This statistic was developed to ensure that water treatment
plants did not violate water quality standards
during droughts (Velz 1984). It establishes a very
low flow that must not be diminished in quality iftreated water is discharged into it. Thus, it requires a high level of sewage treatment but does
not address the flow requirements of fish.

The Tennant Method
The most renowned of the long-range planning
tools for fisheries is that of Tennant (1976). In its
original form, the Tennant Method arrays flowlevels for seasonal periods based on percentagesof the mean annual flow. Tennant used 10 yearsof personal observations in Montana and the midwest to categorize streams into varying quality
trout habitat based on recorded flow. He also
recommended that periodic high flows be provided
to remove silt, sediment, and other bed material.
The U.S.D.A. Forest Service has argued that anannual high flow event is needed to protect thechannel structure in alluvial streams (U.S.D.A.
Forest Service 1984). Because Tennant had inmind more of a scouring purpose, his approach
was not based on these morphological considerations.
Table 2.2 shows Tennant's recommendations
for stream flow to support varying qualities of fish
habitat based on his observations of how to best
mimic nature's hydrology. Some states recognizethat they cannot apply Tennant's recommendations to their own streams without adjustments.
In these cases, changes are made for the species
of interest and the types of streams in a particularstate.
Tennant's method and other desk-top tools anticipate that hydrologic records are available;
when they are not, instream flows can still berecommended based on a surrogate indicator.
Drainage area is an example of such an indicatorfor managed streams. In one drainage area technique, a minimum instream flow value, or baseflow, of 0.5 cubic feetyer second per square mile
(cfsm; 0.0055 cms/kin') of drainage area is recommended for the summer months. Higher flows infall and spring are used to accommodate thespawning and incubation of anadromous species(Larson 1981). Use of this technique for nonanadromous species would, of course, require adifferent set of rules.
These simple, rule-of-thumb techniques
are very useful in the development of long-range

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 11

Table 2.2. Instream flow analysis based on the Tennant method (Tennant 1976).
Percent of mean annual flow
Health of habitat
Flushing or maximum
Optimum
Outstanding
Excellent
Good
Fair
Poor
Severe degradation

October-March

April-September

200
60-100
40
30
20
10
10
<10

200
60-100
60
50
40
30
10
<10

planning recommendations, though they may be
criticized for technical reasons (Kulik 1990). A
more difficult question arises when a problem iscast as long-range planning but is clearly destined
to become an intense negotiation within a very
short time. This change sometimes develops because decision makers do not understand instream flow analysis and believe that a simple
one-time answer will accommodate a complex project. At other times, policy requires a level ofanalytic effort commensurate with some larger
public purpose. While the call goes out for a speedy
recommendation, the expectation is for a sophisticated answer.

Mid-Range Techniques: A
Little More Than BasicStandard-Setting But Not
Quite Incrementalism
Modified Tennant Approach
At the lower end of stream flow quantification
problems for fisheries, where the controversy is
not intense but time is nevertheless a constraint,
a specially tailored Tennant approach might beapplied. This approach calls for the repetition of
all of Tennant's steps. The analyst would begin byobserving habitats known to be important in thespecies' life history and by studying the stream
during flows approximating various percentagesof the mean annual flow. After collecting data on
cross-sectional width, depth, and velocity of thestream at each flow, a set of recommendations
could be made to resemble the set shown in Table 2.2. The difference would be that the new table
would reflect the empirical observations of theanalyst, instead of Tennant, and would be tailoredspecifically to the species and stream of interest.

Wetted Perimeter Technique
The wetted perimeter technique (Nelson 1980)
is another method frequently used with some success, in Montana and elsewhere. In this hydraulicapproach, a desired low-flow value is chosen froma habitat index that incorporates stream channel
characteristics (Trihey and Stalnaker 1985). The
wetted perimeter technique selects the narrowest
wetted bottom of the stream cross section that is
estimated to protect the minimum habitat needs.
The relation of wetted perimeter to cross section
is shown in Fig. 2.1.
The analyst selects an area assumed to be critical for the stream's functioning (typically a riffle)
as an index of habitat for the rest of the stream.
When a riffle is used in the analysis, the assumption is that minimum flow satisfies the needs forfood production, fish passage, and spawning. The
usual procedure is to choose the break or 'point ofdiminishing returns' in the stream's wetted perimeter versus discharge relation as a surrogate forminimally acceptable habitat. This inflection point
represents that flow above which the rate of wetted
perimeter gain begins to slow. Once this level offlow is estimated, other habitat areas, such as pools
and runs, are also assumed to be satisfactorily
protected. Because the shape of the channel can
influence the results of the analysis, this technique
is usually applied to streams with cross sections
that are wide, shallow, and relatively rectangular.
Other fisheries-related standard-setting methods in this middle ground include the Arkansas
Method (Filipek et al. 1987), Hoppe Method(Hoppe 1975), and Texas Method (Mathews and12

BIOLOGICAL REPORT 29

Wetted Perimeter Method

Fig. 2.1. Use of the wetted perimeter
method to estimate instream flows.
Inflexion point

Discharge (efs)

Bao 1991). Additional methods are described by
Wesche and Rechard (1980).

Multiple Attribute Standard-Setting
Methods
All of the methods previously discussed result ina single stream flow value, recommended for adefined period in individual streams. These methods have given rise to the term 'minimum flow:
Such standard-setting recommendations are hard
to use in negotiation because too little information
is available to allow an informed compromise.
Much more must be done to answer the hard questions during negotiation (Wilds 1985). Answering
these hard questions requires moving away fromtools leading only to minimum flows. Techniques
need to show the relation between the amount of
habitat and stream flow. Such approaches allow theanalyst to display impacts on the resource of interest for any given flow.
Tools that can be used to achieve this result fall
into two groups. The first uses statistical analyses
to correlate environmental features of a stream
with fish population size. An example of this typeof analysis is Wyoming's Habitat Quality Index(HQI), described by Binns (1982). An HQI is developed by regressing several habitat variables
against the standing crop of fish. This procedure is
stream-specific, and the recommendations are related to critical low flows. The second group of tools
link open channel hydraulics with known elementsof fish behavior. Examples include the PhysicalHabitat Simulation System (PHABSIM), as firstpresented by Bovee and Milhous (1978) and discussed again by Bovee (1982; also see Milhous et al.

1984). An important explicit element of PHABSIM
and HQI is an analysis of water supply. A watersupply analysis should accompany any standardsetting technique to answer the question: What is
the likelihood that water will be available to meetthe standard?
Many people confuse IFIM with the Physical
HABitat SIMulation System (PHABSIM).
Whereas IFIM is a general problem-solving approach employing systems analysis techniques,
PHABSIM is a specific model designed to calculate
an index to the amount of microhabitat available
for different life stages at different flow levels.
Developed from techniques used in the PacificNorthwest, PHABSIM requires the collection offield data on stream cross sections and habitatfeatures, hydraulic simulation to evaluate habitat
variables at different flows, and species suitability
criteria to calculate stream characteristics withavailable habitat at alternate flows. Depending on
the complexity of the proposed project and thecomplexity of the stream under study, the collection of field data ranges from inexpensive andquick to costly and time consuming.
Using PHABSIM enables the investigator to inform decision makers about the impacts on fish
habitat of different flows for different life stages.
Attention is typically given to the life stages of fish
species that are of special concern for management
or that are thought to be most sensitive to change.
The resulting relation between flow and habitat,
generated by linking species criteria with flow-dependent stream channel characteristics, aids innegotiation by more clearly depicting the effect thatless-than-optimum flow will have on habitat (Geer1980). Figure 2.2 is an example of a typical habitat

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 13

Output of Microhabitat Model(reach specific, life stage specific)

Life stage specific

Flow (cfs)Fig. 2.2. Flow-habitat relation developed by using
PHABSIM.

versus flow function showing how incremental
changes in flow result in quantifiable changes inhabitat value.
Even the best mid-range techniques leave theanalyst open to criticism. There are two frequently challenged features of PHABSIM. First is
the necessity for species suitability criteria (estimated species responses to stream variables, normalized onto a response curve). Figure 2.3 depicts
example suitability criteria for two life stages ofbrown trout. The curves show that adults use
deeper and faster water than do juveniles. These
criteria may be established by several methods
ranging from solicitation of expert opinion to sitespecific collection and verification of field data
(Bovee 1986; Modde and Hardy 1992, (Thomas
and Bovee 1993). All of the criteria development
methods have been challenged to some degree.

The second criticism concerns the requirement toanalyze habitat species by species, which may notaccount for habitat selection affected by interspecies competition (Ross 1986; Hearn 1987; Moddeet al. 1991). Note that the quality of habitat suitability data, along with the significance of PHABSIM's driving variables (e.g., depth, velocity, substrate material, and cover), forms the basis formost criticisms of this technique (Morhardt 1986).
To satisfy such criticisms, more in-depth analysis
is needed than is usually undertaken in simple
PHABSIM or HQI studies. PHABSIM is an incremental method in the sense that it predicts
changes in habitat resulting from changes in flow,
but it focuses on only a few variables affecting
localized fish behavior and ignores the dynamics
of habitat through time. The use of PHABSIM
alone also ignores many other biotic factors suchas inter- and intra-specific interactions.

Incremental Techniques
The mid-range techniques essentially provide
temporal snapshots of stream resources. When theimperatives of negotiation or court proceedings require a more dynamic look at the instream flowquestion, other techniques are needed. These project bargaining problems have been labeled 'incremental' (Trihey and Stalnaker 1985) because adeep knowledge of how aquatic habitat valuechanges as a function of incremental changes instreamflow is required. This detailed quantification must be developed to prepare for negotiations

Brown Trout (Adult)
1.0

Trl 0.5
A
0.0

Fig. 2.3. Suitability-of-use curves for

Brown Trout (Juvenile)brown trout.

1.0

0.5

0.0
Depth (ft.)

5
Velocity (fps)ioChannel index

14

BIOLOGICAL REPORT 29

that involve assessment of the impacts of alternative project proposals.
Incremental problems often create a labyrinthof choices for the analyst who tries to anticipate
questions and design stream flow research to accommodate likely needs. A simple PHABSIM or
HQI analysis will not be sufficient in this setting.
New steps, however, can sometimes be added to
mid-range processes to help them fit more demanding problems. More often, as Olive and Lamb(1984) reported, a more comprehensive approach
must be chosen. Although fish habitat is still thedecision variable, when these more complex tools
are used the analysis alone may require as long as
2 years to complete. Each study is preceded bynegotiations covering study design and followed bynegotiations in which results are debated. The
total elapsed time for study design, data collection,
and analysis may be more than 3 years. Replicate
habitat sampling, biological sampling to develop
habitat suitability criteria, and sediment andwater routing studies, as well as physical habitat,
temperature, and water quality simulations, may
be necessary to accurately depict the effects ofproject operations (Sale 1985). These steps go far
beyond what might be accomplished solely with
PHABSIM.
The IFIM is one process designed to accomplish
this intricate research based on knowledge of fish
response to habitat features. Trihey and Stalnaker(1985) pointed out that processes like IFIM should
be properly called methodologies rather thanmethods. Whereas 'method' connotes a single toolor concept, 'methodology' implies the linking ofprocedures, perhaps from several disciplines, totackle a multi-faceted problem.
In IFIM, habitat suitability data come in two
forms: maerohabitat and mierohabitat. Macrohabitat suitability refers to variables that varylongitudinally downstream, such as water quality, channel morphology, discharge, and temperature. Microhabitat suitability refers to the same
variables used in PHABSIM analysis: depth, velocity, substrate material, and cover. IFIM uses
computer software to integrate these two measures of habitat into habitat units that are thenrelated to flow over time, resulting in a Habitat
Time Series. Figure 2.4 illustrates an example
habitat time series and a population-size timeseries. Note that the population does not track themagnitude of the habitat trace, but rather is afunction of the habitat capacity established by theminima.

Time Series of Populationand Habitat Data--a Limiting habitat event----a Population size or growth
100X

'14\

(M

a

FI
o-

o

3

6

6

6 lb

Years

FIG. 2.4. Example fish population size related to usable
habitat area using the IFIM.

The Habitat Time Series displays the availability of suitable habitat over a period of record. For
example, if the period of record is 10 years (a goodminimum number), the Habitat Time Series would
display available habitat over that 10-year period.
The time trace can be hourly, daily, or monthly.
The analyst can answer many questions, such as
What amount of habitat is available 90% of thetime? What is the median habitat value? Whatwould happen to the available habitat if the flow
were reduced by 20% in high flow months? This
information makes it possible to analyze the effects of changes in flow on each life stage of every
species for which habitat suitability data are available. Where a standard-setting approach might
result in a set of annual or seasonal minima below
which flow could not fall, an incremental techniquemight result in a set of monthly or weekly flowenvelopes, or windows, within which flow mightvary depending on the water supply.
With a complex technique such as IFIM, ananalyst must be able to document the scientificacceptance of all the technologies used and must
be able to extrapolate from the data collected.
Especially in intense negotiations, the assumptions of each method should be well understood,
and careful planning should anticipate what special studies or modifications to a methodology areneeded. The result should be the ability to predictchanges in habitat over time, to make recommendations for wet and dry situations, and to quantify
habitat duration phenomena similar to the firmyield concept in hydrology (Trihey 1981). Figure
2.5 illustrates the duration concept, which summarizes the availability of habitat values acrosstime. For example, at least 15.5 habitat units areTHE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 15%of time exceeded

1 00

90

so
70 -

Baseline•• .•• ........
I'toJect w fl. m --•••
itigation

60 50 -

4030 20 -Project

10 -

o

,
.
00 3.1 6.2 9.3 12.4 15.5 18.6 21.7 24.8 27.9 31.0

Units of available habitat
Fig. 2.5. Duration analysis of habitat available underbaseline conditions, with-project, and after
mitigation of project.

present about 90% of the time under the baseline
condition, but only 15% of the time under the
with-project condition.
An extension of these incremental, project-bargaining methodologies leads to predicting population responses to flow changes (Cheslak and Jacobson 1990; Bartholow et al. 1993). In an approachsuch as IFIM, these predictions will typically require hydrologic analyses, habitat models, sediment transport, water quality, and temperature
analyses, as well as trophic level studies, validationof species criteria, studies of biomass, and population dynamics (Bovee 1982).
An alternative to combining these models intoa predictive methodology would be long-term empirical observations of fish behavior. Such studies
would document population responses to carefully
controlled changes in flow over perhaps 20 years.
Recent research on the South Platte River, Colorado, by Bovee (1988) demonstrated the rigorous
analysis required to show the relation between
flow and population. Bovee's work highlights thatthese relations can be established in theoreticallysound, intuitively satisfying directions. We havealready seen (Fig. 2.4) the form that these population responses to changes in flow over time arelikely to take.

early stages of planning throughout the country.
The wetted perimeter and conceptually similar approaches, concentrating on passage for upstream
migrating salmon, are important first-cut analytical tools. The PHABSIM method is commonly used
as a way to look at hydroelectric power projects(Bovee 1985), to set standards for controversial
streams (Washington Department of Ecology
1987), and to develop conditions on federal permits
and licenses (Cavendish and Duncan 1986). The
PHABSIM method is sometimes used in very complex problems (Olive and Lamb 1984), but caremust be taken to consider several intervening variables. IFIM is appropriate for the most controversial project assessments (Fig. 2.6; Trihey and Stalnaker 1985).
Naturally, all of this experience with instream
flow technology has led to a literature of evaluationand criticism. In particular, useful insights intochoosing and employing instream flow assessment
technologies were provided by Wesche and Rechard (1980), Bain et al. (1982), Orth andMaughan (1982), Loar (1985), Morhardt (1986),
and Gore and Nestler (1988).
In conclusion, experience and the critical literature teach that there is simply no one best way. The
choice of method or methodology depends on thecircumstances. Literally dozens of approaches,models, and tools have been used, each developed
to satisfy a specific need. To establish the necessary
flow, the analyst must know the history and purpose of these techniques and must use this knowledge to make an informed choice of the best process
to follow.

Incremental vs. Standard Setting
Problems

Incroments1

Complexityof decision

Conclusion
Several instream flow quantification procedures
are commonly used. The Tennant Method and wetted perimeter technique are widely used in theStandard
setting

Complexityof system

Fig. 2.6. Spectrum of problem-solving methodologies.

16

BIOLOGICAL REPORT 29

Chapter 3. Ecological Underpinnings
of IFIMIFIM is based on the analysis of habitat for
stream-dwelling organisms under alternative
management treatments. One could logically question why habitat was chosen as the decision variable in IFIM when there are so many other factors(such as stream productivity or fishing mortality)that can potentially influence fish populations.
The simplest reason for basing the analysis on
habitat is that IFIM was designed to quantify
environmental impacts, and impacts to habitat are
the most direct and quantifiable.
The more germane reason for basing IFIM on
an analysis of habitat, however, is the progressionof ecological studies that have implicated or directly shown that habitat is an important determinant of the distribution and abundance of fishes
and aquatic invertebrates in streams. Though recent studies have concentrated on the microhabitat requirements of individual species and life
stages, stream habitat studies have their origins
in community ecology. Detailed information aboutlife history requirements has led to the identification of key physical features of their habitat (e.g.,
depth, velocity, substrate material), quantificationof their importance, and methods to estimate how
they change as a function of stream flow.

contrast, a mature stream had a lower gradient, ameandering pattern in smaller bed material, anda less variable hydrograph. Longitudinal succession was based on the observation that species
distribution and abundance also graded up anddownstream, corresponding to Davis' stream-age
classifications. Refer to Fig. 3.1.
Later authors tried to determine possible
mechanisms or associations relating the faunaldifferences along the longitudinal profile with specific characteristics of individual locations. Trautman (1942) and Huet (1959) found that gradient
was a good predictor of faunal regions, whereas
Burton and Odum (1945) emphasized the effect oftemperature along the headwater-to-lowland continuum. Going downstream in small watersheds,
species were added to the assemblages rather thanreplacing other species. In contrast, species replacements occurred where distances were sufficiently large to create temperature barriers or
where specific types of habitats were not present.
However, studies of longitudinal succession weredistinctly one-dimensional in that they did not
attempt to distinguish the effects of temperaturefrom the associated effects of habitat structure andcomplexity.

Longitudinal Succession

Habitat Segregation

Some of the earliest works relating the distribution and abundance of stream.fishes to their habitat were conducted by Forbes (1907) and Shelford(1911). Shelford (1911) introduced the idea of 'longitudinal succession,' which he compared to a contemporary geologic theory developed by Davis(1909). Davis conceived the idea that the landscapedevelops systematically through erosional stagesof youth, maturity, and old age. Headwater
streams were considered 'young' and characterized by high energy and erratic behavior. A
youthful stream was steep, had a relatively
straight channel with large bed material, and typically exhibited a highly variable flow regime. In

The study of stream habitats on a two-dimensional scale developed as investigators observedthat species tended to segregate by habitat typewithin the same longitudinal zone. Thompson andHunt (1930) were among the earliest researchers
to document the use of different habitat types bydifferent species in short lengths of stream. Theirstudy documented that fish communities tended tosegregate by habitat type based on velocity, depth,
substrate material, and cover type.
Hubbs (1941) postulated that the morphologicaland behavioral characteristics of stream-dwelling
fishes were reflections of the habitat type inwhich the species most typically occurred. He

THE INSTREAM PLOW INCREMENTAL METHOLDOLOGY

Trout

Cold
water

High D.O.
High gradient

Low nutrients
Large bed
materials

17

Detritalfood base

Smallmouth bass

Medium sized
bed materials

Moderate gradientCool waterIntermediate nutrients

Channel catfish
Low gradientHigh nutrients

Warm water
Sandy bed
Low D.O.
Phyloplankton food baseFig. 3.1. Longitudinal succession schematic. Shading denotes approximate gradient from headwaters to intermediate
stream to mature river.

made particular note of a fish's adaptations forinhabiting areas of high velocity, such as streamlined body shape, expansive fins, and specialized
mouth. Similar observations of the distributions ofaquatic invertebrate species were documented by
Sprules (1947). These investigators concluded thatbottom type (substrate material) and velocity werethe most significant determinants of invertebrate
production and diversity in streams.
During the 1960's and 1970's, researchers
learned that the distributions of fish and invertebrates were not random, even within the same
habitat types, and began to investigate determinants of microhabitat selection (see Fig. 3.2). The
three most commonly cited mechanisms involved
reproductive success, energetic advantage, and biotic interactions (competition and predation).

Reproductive SuccessTop (plan) view

Side view
IA Fast water

El Slower water• Riverbed

Salmonid redds are typically located in areas
with clean gravel, with enough velocity to prevent Fig. 3.2. An example of microhabitat specificity.

18

BIOLOGICAL REPORT 29

sediment deposition on the redd, and with the rightcombination of depth and bed form to ensure movement of water through the redd (Hooper 1973).
Locations for redd construction are apparently selected because they provide the best conditions for
incubation and hatching success. Rates of intragravel flow, water exchange between stream andgravel, and dissolved oxygen concentrations areimportant determinants of hatching success in salmonids. The exchange of water (measured as apparent or interstitial velocity) is directly and indirectly related to hydraulic conditions that enhance
percolation through the redds (Coble 1961; Silver
et at 1963). Embryonic survival of steelhead wasfound to be significantly correlated with apparent
velocity and intragravel dissolved oxygen concentrations (Coble 1961). Gangrnark and Bakkala(1958) and Wickett (1954) likewise related salmon
egg survival to dissolved oxygen content and intragravel velocity. Coble (1961) learned that the velocity of subsurface flow was mostly a function of
hydraulic head and permeability. Hydraulic headis a function of the current's depth and bed form;
the head creates a differential water pressure
across and through the spawning bed. Permeability is related primarily to bed particle size and theamount of fine sediment occupying the interstitialspaces among the larger materials. Velocity anddepth are important determinants of both bed particle size and the embeddedness of fine materials,
thus influencing permeability.
Although the relations between rnicrohabitatand spawning success are well documented in salmonids, many species of minnows spawn in microhabitats similar to those used by salmonids. These
include chubs (Leonard et al. 1986; Lobb and Orth
1988), fallfish (Hubbs and Cooper 1936; Carbine
1939), and squawfish (Tyus 1990). Other species,
such as stonerollers, daces, darters, and shiners,
are known to spawn on the nests constructed byhornyhead and bigmouth chubs (Lachner 1952;
Lobb and Orth 1988). This phenomenon led Lachner (1952) to suggest that the use of chub nests byother cyprinids for breeding purposes may be important in the maintenance of a large forage basefor piscivorous species.
Spawning locations selected by centrarchids
bear little resemblance to those chosen by salmonids but are also selected to maximize reproductive success. Whereas many species choose spawning locations with appreciable water movement
through or over the substrate material, centrarchids characteristically select areas near someform of instream cover where the velocity is zeroor near zero (Newcomb 1992; Lukas 1993). Water
movement over the nest greater than about 0.15
foot per second is often a significant cause of reproductive failure in smallmouth bass in lakes (Goff
1986) and in streams (Winemiller and Taylor 1982;
Reynolds and O'Bara 1991). Lukas (1993) concluded that the primary cause of reproductive failure for smallmouth bass in the North Anna River(Virginia) was high flow. Some nests were destroyed by siltation during flood events, but more
typically, when the velocities over the nest site
increased, the guardian male abandoned the nest,or the eggs and larvae were washed away. Similar
spawning behavior has been observed in othersunfishes. Rock bass and redbreast sunfish use
spawning habitats that are similar to those usedby smallmouth bass (Monahan 1991; Lukas 1993).
Reproductive failure in redbreast sunfish was also
linked to high water velocities over nests (Lukas
1993) by mechanisms similar to those found forsmallmouth bass.

Energetics
Riverine environments are distinguished fromother types of aquatic habitat by the presence of acurrent. Velocity is arguably the most significant
abiotic factor affecting the energetics of stream
communities, whether at the level of algal communities, aquatic invertebrates, or fish (Sprules 1947;
Whitford and Schumacher 1964; Bovee 1975). If anorganism is not morphologically adapted for living
in currents (such as through streamlining, buoyancy control, attachment mechanisms, or otheradaptation), it will adopt a behavior of seeking low
velocity areas to reduce individual energy demands (Hubbs 1941). Many species of fish avoid
velocity by occupying pools and locations in thewater column near the streambed. Others makeheavy use of instrearn cover or burrow into thesubstrate material to avoid energetic expenditure.
McCrimmon (1954) observed that habitat requirements of fish change as they grow, with a general
movement into deeper, faster water.
For drift-feeding fish, a resting location of low
velocity in proximity to an area of higher velocity
is advantageous because proportionately more
food will be delivered to the resting location(Fausch and White 1981). Kalleberg (1958) foundthat territories were smaller in riffles and rubble
than in pools, leading to speculation that fish
require less space in high velocity water because
the amount of food passing a given point in theTHE INSTREAM FLOW INCREMENTAL METHOLDOLOGY

stream is proportional to velocity. Chapman

19

distributed along gradients of depth and velocity
in a riffle composed of uniform substrate material.
Minshall and Minshall (1977) suggested seconpetition for food: "Social status confers definite dary feedback mechanisms between velocity andbenefits on individuals. . despotic fish in hierar- substrate material in providing greater surface
chies or successful territorial fish grow more rap- area for habitation on the streambed and in deteridly than subordinates or refugees." Chapman mining the distribution of food materials foralso postulated that a similar principle operated macroinvertebrates.
Although many species select and compete forat the invertebrate level, thereby forming a link
between habitat and the fish food supply. These microhabitats that optimize foraging energetics,
are important concepts relating to the argument prey species often select microhabitats that reduceover food limitations or space limitations in their risk of predation. Whereas territorial expanstream populations. Chapman's (1966) study indi- sion often occurs when a dominant competitor iscates that in territorial animals, food limitations removed from the system, a similar phenomenon
may be shown to be actually space limitations in has been observed in prey species when a predator
the form of competition over larger and higher is removed. Gilliam and Fraser (1987) proposedthat animals do not select microhabitats by maxiquality microhabitats.
The energetically advantageous behavior of mizing energetics or reducing predation hazard
feeding from a low energy' location with forays independently. Rather, locations are selected that
into 'high energy' locations is not confined to sal- minimize the ratio between mortality rate andmonids. Lobb and Orth (1988) reported a nearly foraging rate. In essence, the most favorable miidentical feeding strategy in the bigmouth chub. crohabitat for an organism would be a place where
They suggested that the microhabitats selected by it could increase its energy input with the least riskof predation. Lewis (1969) concluded that stream
the chub not only presented the greatest energetic
trout populations were determined largely by theadvantage, but also minimized the risk of predaquality of the habitat; velocity was important as antion by birds and fish. Stream-dwelling fish thatenergetic mechanism, but cover was related to aambush their prey, including many centrarchids
photonegative response and to predation avoidand esocids, tend to select low energy areas assoance. Power (1984) observed that armored catfish
ciated with complex structural cover (Haines andavoided shallow areas during the daytime, alButler 1969; McClendon and Rabeni 1987; Monathough their food is abundant there, and suggested
han 1991). These species tend to select cover types
that these areas were avoided because of susceptithat provide a shelter from the current and accen- bility to avian predators.
tuate a contrast in lighting; ambushes succeed
better if initiated from a dark area into a well-lit
Habitat Bottlenecks
area (Helfman 1981). Probst et al. (1984) notedthat smaller smallmouth bass often were observed
Wiens (1977) coined the term ecological bottleoccupying positions adjacent to moderate velocity, neckto describe mechanisms by which communias if feeding on drifting invertebrates.
ties of organisms are regulated by temporally
Some species (such as darters, daces, sculpins, variable, environmentally induced phenomena.
and madtoms) tend to occupy microhabitats An ecological bottleneck has the effect of depresswhere their food supply is greatest (Hynes 1970). ing potentially competitive populations well below
Morphological and behavioral adaptations are the carrying capacity. Once the restriction is realso common in stream-dwelling rnacroinverte- lieved, competition is reduced or eliminated bebrates. Some species of mayflies exhibit extreme cause adequate resources are available for the
dorso-ventral flattening, which allows them to standing crop that remains. A habitat bottleneck
creep around in the laminar sublayer on top of and is similar to Wiens' (1977) definition, but refers
between rocks in torrential currents. Some spe- solely to habitat limitations that affect populacies have suction devices to hold them in place on tions of individual species (refer to Fig. 2.4),
the substrate material. Still others, notably the rather than the community as a whole. In contrast
stoneflies, must live in a current because their to longitudinal succession and habitat segregagills are immovable and cannot exchange oxygen tion, which focus on spatial distributions, the priin standing water (Usinger 1956). Needham and mary dimension embodied by the habitat bottleUsinger (1956) found that aquatic insects were neck concept is the element of time.
(1966) suggested that the defense of territories
exhibited by salmonids was a surrogate for com-

20

BIOLOGICAL REPORT 29

Habitat bottlenecks are important, but sometimes poorly understood. The basic premise of thehabitat bottleneck is that populations of aquaticorganisms are related to the availability of habitat
through time. This definition has been commonly
misinterpreted to mean that adult fish populations must be instantaneously correlated with
habitat. Such an interpretation logically requires
a belief in instantaneous mortality and spontaneous generation, or the ability of fish to movequickly among habitats, in order for fish populations to increase and decrease at the same ratethat habitat can change in a stream. In reality,
habitat limitations affecting a population usuallyoccur prior to the time when the population size
is measured. Adult populations are frequently
determined by recruitment, which is highly correlated with the amount of habitat available forearly life stages of the species. Such 'habitat
events' usually affect recruitment via habitat
types directly related to the production and survival of eggs, larvae, and fry (such as spawning
habitat and young-of-year rearing habitat), or indirectly related to survival by the growth rates ofage-0 fish (such as temperature regime, young-ofyear rearing habitat, or microhabitat for invertebrate food supplies). These habitat bottlenecks
typically occur 1 to 3 years prior to maturation,
when their effects are detectable in the adult
population (Nehring and Anderson 1993; Boveeet al. 1994). In addition, Bovee et al. (1994) foundthat
1. there may be several consecutive and independent habitat events that can affect adult
populations (such as spawning habitat, fry
rearing habitat, temperature regime, and adultfeeding habitat);
2. limiting events frequently occur over variable
time scales (such as acute events that limit fry
survival versus chronic events, such as longterm crowding of adults during the summer);
3. habitat may be limited by both high and low
flow events and by the rate of change of flow
events;
4. the smallest amount of habitat available during
the year may not necessarily be the limiting
event (such as during the winter when fish areinactive); and5. habitat types not directly utilized by the species(such as macroinvertebrate habitat as it affects
food supply for fish) may be more important
than the habitat directly used by the species.

Conclusion
A common misinterpretation of IFIM is that itis only a 'trout model.' This misunderstanding isundoubtedly related to the origins of the techniquefor quantifying salmonid microhabitat (Collings
et al. 1972), which formed the conceptual basis for
the Physical Habitat Simulation System (PHABSIM). Although the modeling techniques underlying PHABSIM originated in salmonid streams,
Bovee (1975) concluded that there were sufficientparallels in microhabitat use across stream communities that the same basic approach could be
used in most riverine environments for essentiallyany riverine species.
As discussed in this chapter, many concepts andcomponents of IFIM are rooted in community ecology and were developed from many stream settings. Students of IFIM should have little trouble
recognizing the influence of the longitudinal succession concept as a defining property of macrohabitat. Longitudinal succession has been confirmed in many studies, in coldwater andwarmwater streams, since Shelford's (1911) original hypothesis.' In IFIM, macrohabitat components such as channel structure and discharge areused to define sampling strata for the quantification of microhabitat. Temperature and water quality are incorporated in IFIM to define the longitudinal limits where a species can or cannot survive.
The treatment of microhabitat in IFIM using
PHABSIM is consistent with the two-dimensional
partitioning of microhabitats documented for
stream-dwelling organisms ranging from algae tofish. Although the reasons for habitat partitioning
may vary, such behavior is commonplace in stream
ecosystems worldwide. One possible reason for theuniversality of this phenomenon is that streams
provide unique but repetitive types of microhabitat
niches no matter where they are, and there will
always be one or more species adapted to fillingthose niches.
PHABSIM has been criticized because it contains only a few variables, namely depth, velocity,and channel index (usually a combination of substrate material and cover). However, in nearly allof the studies conducted on habitat partitioning
among stream-dwelling animals, these variables
were consistently found to be important determinants of species distributions and abundance. The
1

The concept of longitudinal succession has matured into what
today is the river continuum concept (Vannote et al. 1980).

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY

emphasis placed on the careful development andtesting of habitat suitability criteria used in
PHABSIM is a recognition that the microhabitat
requirements by some (not all) species are flexible
and can be modified by species interactions suchas competition and predation.
The habitat time series is based on the fact thatdecisions related to habitat and water management must address the temporal variability ofriverine environments. Habitat bottlenecks are
difficult to identify without an abundance of hydrologic-, habitat-, and population-related data.
Nevertheless, the existence of habitat bottlenecks
has been demonstrated in cold- and cool-water
stream environments. Studies in community ecol-

21

ogy provide evidence that they also exist in warmwater streams. Therefore, the idea of using a
habitat time series to relieve potential habitat
bottlenecks, avoid exacerbating them, or (rarely)
amplify them is a reasonable approach to the
problem of temporal variability. A more fundamental argument for employing the habitat timeseries is that temporal evaluations are routine in
the water management disciplines. The habitat
time series allows the presentation of biologicalinformation in a format that is familiar to water
managers and engineers. IFIM is unique among
habitat assessment tools in that it fosters thesimultaneous examination of habitat variability
over time and space.

22

BIOLOGICAL REPORT 29

Chapter 4. Philosophical
Underpinnings of IFIM

Certain philosophical principles have guided
the development of IFIM and help explain its organization and intended use. These include principled bargaining, incrementalism, interdisciplinary problem-solving, and craftsmanship. In
addition, the problem-solving approach, based on
ecological theory, guides us in dealing with complex and contentious issues and helps us continuelearning about ecological systems.

AxiomsPrincipled bargaining recognizes and attempts
to accommodate the values of every legitimate
stakeholder in an instream flow case. This idea
also stipulates that the best solution to a problem
is derived through mutual agreement of negotiated issues. A hard realization of this philosophy
is that the methodology is neutral; it can be usedequally well to represent a developer's viewpointor that of a conservation group. However, properuse of the methodology requires that all legitimate concerns be addressed. IFIM can be used toevaluate a problem from only one perspective, butsuch an approach carries substantial risk. Failure
to incorporate all legitimate concerns in the formulation of alternatives may result in a solutionthat creates more problems than it solves. Suchalternatives are likely to be vigorously contested
by stakeholders who perceive that they have beenleft out.
Incrementalism is based on the observation that
individuals and groups solve problems as they
have solved problems in the past. Without a truly
traumatic experience, we will not radically alter
our value systems, our missions, or the way weassimilate and use information. Changes in thesehuman factors occur in increments. The way wesolve the next problem will look pretty much likethe way we solved the last similar problem, withperhaps a little movement or flexibility in a particular direction. Incrementalism applies to IFIM
through the process of iterative problem-solving.

It is almost inconceivable that the perfect solution,
optimizing for all legitimate concerns, will be discovered on the first try. Rather, solutions are derived by starting with a plausible alternative andthen tinkering with it until everyone is as satisfied
with the outcome as possible. People unfamiliar
with instream flow problems or IFIM are often
concerned about the acceptance of IFIM by the
courts, but IFIM does not stress litigation. Though
IFIM has recently been accepted as a legitimate
methodology by the U.S. Supreme Court, the vast
majority of instream flow problems (we estimate
around 99%) are resolved through negotiation
rather than arbitration.
IFIM is an interdisciplinary tool requiring different skills and expertise throughout its implementation. Competence in political science, negotiation, and law is crucial when designing studies
and preparing for negotiations. Experience inwater management and hydrology is crucial in
preparing alternatives that are physically feasible
to implement. The ability to relate habitat phenomena to biological populations is essential todetermine whether an alternative will result in abeneficial, detrimental, or neutral outcome. Simply collecting the data and running the models
associated with IFIM may require skills in hydraulic engineering, biology, temperature modeling,chemistry, and geomorphology. The obvious valueof interdisciplinary teams is that one person does
not need to know how to do everything. Less obvious, however, is that different disciplines often use
different strategies and logic in problem-solving.
By incorporating multiple disciplines in a team,the opportunity exists to formulate innovative solutions that might not have been considered by ahomogeneous group.
Craftsmanship refers to the fact that IFIM is ascientific approach to problem solving, but IFIM is
not science. Its purpose is to help disparate groups
resolve complex, multiple-issue problems in a systematic yet flexible manner. IFIM is based on thescientific method, but also relies on assumption,

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 23

subjectivity, and judgement. It is something thatcan only truly be learned by doing. Trust andcredibility are essential to the implementation of
IFIM, and they must appear in every application.
Our knowledge about rivers, biology, and humannature will never be perfect, nor will our implementation of IFIM. We can, however, control thequality of our own work. We can be craftsmen.

Approach
IFIM is an adaptive system composed of a library of models that are linked to describe thespatial and temporal habitat features of a given
river regulation. In addressing a river systemproblem, one must keep in mind the matter ofscale. Table 4.1 describes a river system at fivelevels of resolution, from the river basin scale down
to microhabitats (similar to that offered by Frissell
et al. 1986). When addressing a river regulation
problem, it is necessary to bound the area of influence and to stratify your approach so that observations can be expanded from the micro-scale up toat least the river segment scale, if not the stream
network or full sub-basin scale. Most experienceand application of IFIM techniques have been at
the micro- and meso-habitat levels, focusing on one
or a few river segments. Consequently, the greatest improvement in field techniques and the most
tested concepts relate to (1) river hydraulics andmicrohabitat utilization by aquatic species and(2) longitudinal analysis of water chemistry andtemperature through long river segments composed of many mesohabitat types.

Recent emphasis on reservoir operations andstream network analysis has linked habitat models
with engineering models for water routing andreservoir storage and release (Waddle 1992). The
combined effects of severe ramping rates associatedwith peaking hydropower operations and the reevaluation of large storage reservoir operations
have elevated the instream flow management issue
in the United States to the stream network andeven the river basin scale (Lubinski 1992; Hesseand Sheets 1993).
A thorough understanding of the hydroperiod,
the water supply, and the management capabilities is essential to IFIM studies in regulated rivers. The most common instream flow problems
being addressed today throughout the UnitedStates require the aggregation of habitat data at
the stream network or sub-basin level and focus
fishery managers' attention to the populationlevel. The inherent need to describe the within-basin movement and life history periodicity(Fig. 4.1) establishes the utility of computer-basedmodeling for tracking and summarizing information throughout a stream network (Bartholow
et al. 1993). It is no longer sufficient to argue forflows to maximize the habitat value for one life
stage (adult) at a few isolated spots in a river.
Computer simulations provide the mechanism for'gaming' with various river regulation schemes.
Allocated water budgets for fish production anddecisions on storage and release from reservoirs
are now becoming the responsibility of the fishery
manager (Waddle 1991; Bartholow and Waddle
1994).

Table 4.1. Major factors influencing habitat of river ecosystems based on spatial scale of the processes.
ScaleRiver basin
Stream network
River segment (macro-scale)

Mesohabitats (meso-scale)
Cross sections (micro-scale)

Major factors influencing habitat
Climatic change; climax vegetation; geologic disturbances (earthquakes,
volcanos); catastrophic floods and droughts.
Valley gradient; local geology (natural or man-made barriers to fish migration);watershed vegetation and land use activities; runoff patterns; groundwater
flow; soils and sediment yield; location of dams and diversions.
Longitudinal gradients of temperature and water quality; habitat types andproportions (more similar within segments than among segments); canyons,floodplain segments, bedrock controlled reaches, alluvial reaches, etc. Periodic
floods can reshape floodplain contours and reroute channels.
Unique channel width/depth ratios: Pools, runs, chutes, oxbows, cutoff
backwaters, riffles, pocketwater, plunge pools, side channels, navigation pools,
channelized reaches.
Channel geometry; stage/discharge relations; substrate material distribution;% fine materials; cover objects (instream, undercut banks, overhead vegetation, ledge rock, woody debris, root wads); depth and velocity distributions.

24

BIOLOGICAL REPORT 29

Periodicity Chart
Jan FabMar Apr May Jun Jul Aug

Adults- summer- winter- spawning
Fry
Juvenile

Habitat Structure

Sew 001 Nov Dec

1
FH

1

Fig. 4.1. Species periodicity chart.
In developing the Index of Biological Integrity(IBI), Gorman and Karr (1978) suggested that human-induced impacts to river systems fall into five
major categories. Table 4.2 (as modified from Karr
1991) identifies food source, water quality, habitat
structure, flow regime, and biotic interactions as
equally important, but very different, mechanisms
by which human activities can alter the biotic integrity of running-water ecosystems. The IFIM
modeling approach has been influenced by thisview of river system impacts, and models have beendeveloped that fit within Karr's paradigm, as discussed below.

Flow Regime
During the 1950's and 1960's, construction oflarge storage reservoirs and massive withdrawal
systems for irrigation in the western United States
focused IFIM developers on techniques for evaluating changes in flow regime. Today, the most sophisticated modeling in the area of flow regime combines ideas from hydraulic engineering, river floodrouting, and habitat-use behavior of fish with empirically measured calibration flows. Hydraulicsimulation models allow for accurate prediction ofwater surface elevations, water depth, and watervelocity at points in the water column and at various points across a river channel. Models allow
simulations of these variables for many unmeasured discharges (Milhous et al. 1989). Such simulations allow the analyst to evaluate the durationand timing of inundation of the aquatic-terrestrial
transition zone (ATTZ; Junk et al. 1989). The flow
regime is also recognized as critical for channel
maintenance, both in terms of maintaining habitat
structure (e.g., stream width, riparian vegetation)and in flushing fine sediment out of gravel/cobble
channels. (U.S. Forest Service 1984)

The influence of human-induced activity on
habitat structure (channel-floodplain geometry)has been one of the most neglected areas of stream
ecology (Hill et al. 1991). At present, riverine geomorphology is at the forefront of descriptive ecology, and much work is in progress. A prime example is the effort of the U.S. Army Corps ofEngineers to restore floodplain channel connections along river corridors that have been severely
impacted through river entrainment for navigation and reservoir operations. The classification ofmesohabitat types, and the association of important species and life history events to those specifichabitats, underscores the importance of adequately describing and manipulating channel morphology as a component of river management.
Many riverine species throughout the UnitedStates are rapidly declining, and many species areproposed for listing as threatened or endangered.
The loss of side channel, backwater, and edge
habitats has been a primary reason for this decline(Hesse and Sheets 1993). There are no predictive
habitat structure or channel models acceptable for
evaluating flow regime in terms of the active channel response. Crude calculations of the extent of
aggradation or degradation (Fig. 4.2) at selectedcross sections below a large reservoir are possible
but cannot be used to forecast channel widening,edge habitat building, or floodplain cutting. There
has been much empirical research on the protection of existing channels (Stalnaker et al. 1989)
and restoration of floodplain habitats (Hesse andSheets 1993). Recently, researchers have focusedinterest on flushing flows as part of river management regime for flushing silts and sands fromwithin the interstitial spaces among gravel andcobbles in trout and salmon streams (Reiser et al.
1989). This research is now progressing into thelaboratory and, along with field studies, should
provide algorithms suitable for computing theamount and timing of flow pulses for flushing finesfrom river reaches below large reservoirs.

Water Quality
There are sophisticated and well-developed
water quality models (Bartholow 1989; Thornton
et al. 1990). Water chemistry, dissolved oxygen(DO), and temperature can be very accurately predicted throughout a stream network system as afunction of reservoir operations and water routing.
However, modeling emphasis has been largely toTable 4 2. Primary ways that human-induced alterations impact river ecosystem biological integrity (modified from Karr [1991]).
Flow regime

Habitat structure

Water quality

Channel geometry
Floodplain connection
Substrate material
Percentage of fines
Meso-type diversity (pools,
runs, chutes, backwaters,
riffles, woody materials)
Bank stability
Cover objects
Riparian vegetation

Temperature
Dissolved oxygen
Turbidity
Nutrients
Dissolved chemicals
Heavy metals and taxies
pH

Food source

Biotic interaction

Particulate organic material
Terrestrial insects
Seasonal pattern of energy
input from floodplain andwatershed

Competition for food andspace
Predation
DiseaseParasitism

Important Variables
Discharge
Water depth
Water velocity
FloodsDroughts
Dynamic inundationof aquatic-terrestrial
transition zone (ATTZ)
during peaking
Sediment transport

Disruptions
Depletion—reduced
minimum flows andvelocities
Storage-reduced
imiundation of AZZT,
reduced energy input
Reduced reproductive
success of floodplain
rearing fish species
Peaking hydro—increased
extremes (magnitude andfrequency of high and low
flows)
Reduced diversity of
depth/velocity
combinations
Reduced feeding stations

Decreased stability of banks Increased or decreased
Isolation of floodplain
Increased siltation overturbidity
and removal of riparian
substrated material
Altered temperaturevegetation leads toRemoval of trees from
regimesdecreases in organic
riparian zone
Altered diurnal dissolved
materials (coarse and fine
Reduced cover-loss ofoxygen cycle
particles
undercut banks andAltered salinity
Increased algal production
woody debris
Increased nutrients, toxics due to input of nitrogen
Isolation of floodplainor suspended solids
and phosphorus
from channel
Altered decomposition rates
Chartnelization—reduced
sinuosity more uniform
water depths
Increased erosion fromwatershed (timbering,grazing, urban sprawl)

Shift in species composition
and abundance-fishes andinvertebrates
Introduction of exotic species
Disruption of seasonal rhythms
Alterations in primary andsecondary productiontrophic structure
Shifts in habitat guilds(increased omnivores anddecreased piscivores)
Increased hybridization among
fishesDecrease in obligate riverine
fish species
Increasing numbers of candidate species for listing as
threatened or endangered

26

BIOLOGICAL REPORT 29

Aggradation

VI'

*Pt

IMF
1970

1990

Degradation

1970

1990

Fig. 4.2. Channel aggradation compared withdegradation.

meet chemical criteria and public health criteria;
little has been done to advance the state-of-the-art
in managing healthy and viable biotic communities within regulated rivers. Nonetheless, temperature and DO can be modeled, and these approaches are useful in designing flow releasepatterns timed to provide optimal conditions forspawning and growth (Armour 1991, 1993a,
1993b). More must be accomplished in this arena.

Food Energy Source
Thus far, flow-related models for evaluating thefood base in stream systems have been predominantly restricted to habitat use by benthic
macroinvertebrates in streams inhabited by trout
and salmon. Such models are based on velocity
relations in the substrate material used by aquatic
insects (Gore and Judy 1981; Minshall 1984; Gore1987), and were recently shown by Jowett (1993)
to account for a significant amount of the variationin brown trout production among 89 trout streams
in New Zealand.

Biotic Interactions
Of the five areas, this one offers most promise
for a research breakthrough in the development ofmanagement tools for application. Species competition as a consequence of flow management has
thus far taken the form of examining the amountof usable habitat overlap among trout species (Nehring and Miller 1987; Loar and West 1992). Careful examination of simulated historical temperature and flow patterns for a stream reach canprovide evidence for mechanisms supporting theobserved dominance of one trout species over another in the reach. Unfavorable temperature during spawning and incubation, unfavorably highvelocities during fry emergence, or large overlap inpreferred space during critical periods may tip thebalance in favor of one species over another. Further research is needed for developing habitat
models based on community structure. Habitat
use guilds for fishes have been discussed by
Leonard and Orth (1988) and Bain and Boltz(1989). There is ongoing research addressing
guilds in southeastern United States coastal andpiedmont warmwater stream systems (Bain and
Boltz 1989; Freeman and Crance 1993).

Stream Habitat as an Integrator ofMan's Influence on Stream Systems
The initial focus of instrearn flow studies using
IFIM models was on understanding habitat dynamics as simulated for recent historical flow conditions in the stream system under study. Analytical procedures developed by scientists at the
Midcontinent Ecological Research Center (formerly the National Ecology Research Center) aid
the river analyst in examining the spatial andtemporal aspects of stream habitat integrity.
These procedures provide information compatible
with three current concepts of stream ecosystems(Table 4.3): (1) longitudinal succession, startingwith the principles introduced in Chapter III and
expanded into the river continuum concept by Vannote et al. (1980); (2) habitat segregation and theimportance of habitat patchiness and habitat
boundaries in resource partitioning; and (3) biotic
responses to stochastic processes such as weather(Wiens 1977; Grossman et al. 1982; Schlosser
1982, 1987). In dynamic stream environments theinteraction of all three ideas into an integrated
analysis of the spatial and temporal aspects of theenvironment is necessary to sort out the relative
importance of deterministic and stochastic processes to the community being studied (Schlosser
1982; Gelwick 1990; Strange et al. 1992).
It is possible to model the linear distribution oftemperature, dissolved oxygen, and importantchemical constituents and to compute the linear
extent of usable macrohabitat, the extent of optimal
microhabitat, or the position of threshold bounds
for limiting variables. Aquatic species distribution
along a river segment continuum can be determined for many well-known aquatic organisms.
Such analyses require adequate sampling of thewater column along the linear distribution of mesohabitat types in the river segments of concern.
Within mesohabitat types, measurements of the
distribution of cover, substrate material, and water
depths and velocities, when linked with hydraulicTHE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 27

TABLE 4.3. IFIM models developed for integrating the spatial and temporal scales of habitat analyses.

River perspective
Longitudinal succession (river continuum)

Habitat segregation and patchiness
Variable meteorological processes

Type of model
One-dimensional macrohabitat models—temperature,
dissolved oxygen, dissolved chemicals. Indicators: degreeday accumulations of temperature, thresholds of tolerance,
extent of optimum or acceptable conditions.
Two-dimensional microhabitat models—depth/velocity
distributions in association with substrate material andcover in small cells.
Time series of the total amount of usable habitat present in
the aggregate over the stream network or a specified
portion. Indicators: seasonal occurrence and duration of
ecological bottlenecks associated with flood, droughts, orhuman-induced hydro-peaking or flow depletions.

simulation, can model the qualities and patchinessof the usable microhabitats. Microhabitat analyses
can identify velocity boundaries important to drift
feeders and velocity barriers to rearing immobile orvelocity-intolerant life forms.
Computer programs (Time Series Library; Milhous et al. 1990) allow the analyst to integrate themacro or longitudinal (one-dimensional) habitat
data with the one-dimensional hydrologic data
throughout a stream system to produce a timeseries analysis of the total amount of usable habitat available for specified species and life stages
for particular periods. The spatial analyses areaggregated at the stream network or sub-basin
level. Evaluations of atypical events (i.e., climatic
disturbances such as droughts and floods) aremade by examining the habitat time series forhabitat bottlenecks; their magnitude, frequency,

duration, and timing of occurrence; and the life
stages they appear to influence. With such historical analyses (back calculations), the analyst is
better able to compare proposed operating alternatives and document the probable impacts of
those changes.
These integrated analyses are termed effective
habitat analyses (Bovee 1982). Effective habitat
analysis and the identification of habitat bottlenecks have become the focus of instream flow studies involving trout and salmon in the western
United States (Bovee 1988). In these analyses, theinvestigator transforms the habitat time series into
a quasi-population model (Waddle 1992). Effective
habitat analyses aid the biologists by allowing themto use population dynamics theory and experience
to interpret the likely outcome of stream water
management options.

28

BIOLOGICAL REPORT 29

Chapter 5. The Application of IFIM

The IFIM is meant to be implemented in five
sequential phases: problem identification, study
planning, study implementation, alternatives
analysis, and problem resolution. Collectively,
these phases encompass the individual steps
shown in the previous flowchart (Fig. 1.1). This
chapter summarizes each phase, telling who themajor players are for each phase and what is to beaccomplished in that phase. Two things should
become apparent as you read about the five phasesof applying IFIM. First, each phase must precede
the remaining phases, though cycling throughthem will be a necessity as projects increase incomplexity. Skipping or minimizing any step islikely to result in an unsatisfactory assessment.
Second, full and open communication is an essential ingredient of each phase. Such communication
will help ensure that all parties accept the IFIM
process and have a positive view of what should bemutually beneficial results. In some ways, communication is an ingredient as well as a product ofeach phase because a successful application of
IFIM should result in mutually acceptable decisions.

Problem Identification
After a proposed change in the water management system becomes known, the first phase of an
IFIM assessment begins. This phase has twoparts, a legal-institutional analysis and a physicalanalysis. The interagency group should performthe legal and institutional analysis. This analysis
identifies all affected or interested parties, theirconcerns, information needs, and relative influence or power, as well as the likely decision process(i.e., Is it more likely to be a brokered or arbitrated
decision?). Thus, phase one will result in a better
understanding of the proposed project, the likely
impacts, and the objectives of all interested parties. This understanding sets the stage for multiobjective planning that will encourage analyses
other than just the proposed project operation.
Also, negotiating the details at an early stage

provides the foundation for continued successful
negotiation throughout the assessment.
In the second part of phase one, the physicalanalysis determines (1) the physical location andgeographic extent of probable physical and chemical changes to the system, and (2) the aquatic (andperhaps recreational) resources of greatest concern, along with their respective management objectives. Problem identification is often accomplished with a s coping meeting involving themanagement and regulatory agencies likely to be
involved with the decision. A preferred alternative
may be identified by the project proponent, and theconsequences of this alternative are translated
into a hydrologic time series that assumes the
project is in place and operating as proposed. The
group should also jointly develop a baseline hydrologic time series representing either the status quoor another baseline that is mutually acceptable.
The two (or more) hydrologic time series, in apreliminary sense, establish the basis for the next
phase—study planning.

Study Planning
Carefully planning the course of an IFIM assessment is critical. The focus of this phase is to
identify what information is needed to address theconcerns of each group, what information alreadyexists, and what new information must be obtained. Study planning details should dominate
the discussions and result in a concise, written
plan documenting who is going to do what, when,
where, how, and for how much money. The study
plan must be feasible, given the decision schedule,
and the human and financial resources available.
The interdisciplinary planning team must buildon the objectives and information needs of eachparty. The team should not try to predict theoutcome of a study but focus on data collection andthe methods to be used. Proper planning will leadto the collective identification of (1) the pertinent
temporal and spatial scale of evaluations, (2) themost important variables for which information isneeded, and (3) how information will be obtained

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 29(e.g., measurement methods, simulation, expert
opinion) if it does not exist. The planning groupmust also agree on methods of quantifying theeffects of each alternative to be analyzed.
The hydrologic information chosen to represent
the baseline or reference condition should be reexamined in detail at this point in the study. All
parties must understand and agree on one or morehydrologic time series that will be used for comparison. The baseline hydrologic time series serves
as a reference point for judging potential impacts.
Often the reference baseline condition is not theactual historical hydrology used in problem identification, but a synthetic time series representing
present water uses, operational procedures, andwaste loads superimposed on the variability foundin the historical hydrologic records. (Occasionally,
the baseline hydrology includes future operational
procedures that are not yet in place but have beenformally approved and are imminent.) Two or morereference hydrologic time series are commonlyused for baseline conditions.
The resource agency responsible for fisheries
must describe the biological reference or benchmark conditions. Identifying the geographic distribution and important times of the year (for spawning, migration, etc.) is critical in evaluating
different life history phases of the fish populations.
A population benchmark may be constructed using
historical habitat conditions (from best estimatesof actual historical hydrology) and `backcasting' toidentify critical events that populations may haveexperienced due to physical or chemical limitations reflected as habitat bottlenecks (Burns 1971).
A written study plan should (1) determine whendata collection must be completed in the field;(2) synchronize the collection of data needed formodel input, calibration, and testing; and (3) estimate the labor, equipment, travel, and other costs
required to produce the needed information by theagreed study deadline. An interdisciplinary planning effort representing all the major interest
groups can result in considerable savings of timeand effort during the conflict resolution phase. A
common mistake in planning is to go about describing a 'set' of data and 'standard collection procedures' appropriate for commonly used models. This
shortcut simplifies initiation of the data collection
phase but often does not build a common understanding of data needed or agreement on the analytical approach. Lack of group planning may leadto polarization of the parties, which may stifle thenegotiation process.

Study Implementation
From the field biologists' and the resource agencies' perspective, the implementation phase isoften the most interesting and scientifically challenging. This phase consists of several sequential
activities: data collection, model calibration, predictive simulation, and synthesis of results. Proper
implementation of the study is critical and canbring biological credibility to the decision process
but will not, by itself, result in good decisions.
During implementation, sampling locations are
selected for collecting empirical data used in predictive models. Data collected can include temperature, pH, dissolved oxygen, biological parameters, and measures of flow such as velocity,
depth, and cover. These variables are used in
describing the relation between stream flow andstream habitat utility. IFIM relies heavily onmodels because they can be used to evaluate new
projects or new operations of existing projects.
Model calibration and quality assurance (Fig. 5.1)
are keys during this phase and, when performed
carefully, lead to reliable estimates of the total
habitat within the study area during simulationof the alternative flow regimes. Total habitat is
synthesized by integrating large-scale macrohabitat variables with small-scale microhabitat variables (Fig. 5.2). An important intermediate product from this phase is the baseline habitat timeseries. This analysis determines how much habitat in total would be available for each life stageof each species over time. The baseline habitat
time series provides the base from which rational
judgements can be made about proposed alternative management schemes.
Inappropriate selection and use of models andfailure to verify model assumptions can lead tomajor errors in application (Shirvell 1986; Scottand Shirvell 1987). Because all habitat-based instream flow models rely on empirical measurements of the stream channel as inputs, adequate
understanding of sediment transport and channel
dynamics must be incorporated into any habitat
time series analysis. If a channel is not in dynamic
equilibrium, the modelers may have to hedge on
simulation of alternative futures and call for periodic adjustments, with empirical measurements atregular intervals.
Some site-specific empirical evidence should becollected to ensure validity when applying instream
flow models to the decision-making process. Sitespecific data help reduce the large amount of uncertainty in understanding how biological systems

30

BIOLOGICAL REPORT 29

SYSTEM INPUTS I

Parameter
estimation± errorrjObserved\ values± error

MODEL(System representation)± errorverification

NATURAL SYSTEM
Fig. 5.1. Calibration process.

- Calibration
parameteradjustment± errorCalibration/
validationModeloutputs

MODEL PREDICTIONS

Observed>4
values± error
Systemoutputs

work and reduce the imprecision of small samples
that are used to represent a dynamic stream system. Site-specific data also foster communication
among the diverse disciplines of engineering, law,ecology, and economics. Just as grab sample measurements of temperature, water quality, depths,
and velocities are routinely used to calibrate physical and chemical models, samples of the aquaticorganisms and their habitat use must be used to'calibrate' the habitat simulations used in IFIM
alternatives analyses.
Properly completed, phase three results in reliable estimates of the relation between flow andtotal habitat, as well as good measures of theamount of habitat available under the chosen baseline conditions and the various with-project alternatives. This habitat quantification leads naturally

Microhabitat

Macrohabitat
Discharge
Temperature -------- \Depth
Velocity

'-„

Water
quality

Channelstructure

Miles of usable stream

X

Substrate
Cover

Habitat area permile of stream= Total Habitat
Fig. 5.2. Total habitat combines elements of macrohabitatand microhabitat.

into the next phase, which will compare and evaluate the alternatives. Before discussing the next
phase, however, it would be best to make specificmention of PHABSIM.

PHABSIM
Many people confuse IFIM with the Physical
HABitat SIMulation System (PHABSIM).
Whereas IFIM is a general problem-solving approach employing systems analysis techniques,
PHABSIM is a specific model designed to calculate
an index to the amount of microhabitat available
for different life stages at different flow levels.
PHABSIM has two major analytical components:
stream hydraulics and life stage-specific habitat
requirements (Figs. 5.3a and 5.3b).
The stream hydraulic component predicts
depths and water velocities at specific locations on
a cross section of a stream. Field measurements ofdepth, velocity, substrate material, and cover at
specific sampling points on a cross section aretaken at different flows. The sampling points arecalled verticals and describe conditions for somedistance around them (cells) judged to be relatively
homogeneous. Hydraulic measurements, such as
water surface elevations, are also collected during
the field inventory. These data are used to calibrate the hydraulic models. The models are thenused to predict depths and velocities at flows different from those measured. It is usually assumed
that the substrate material and cover do notchange at different flow levels, but this assumption
is not required.

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 31

to
0.8
— 0.8

en

Cross section B

9.4
0.2
0

1111100 1 2 3 4

Velocity (ftisec)
1.0
0.8

9

0 1 2

3

4

Depth (ft)

0.8
0.4
0.2

100,000
A

Seasonal relation
between discharge
and microhabitatfor each We stagee/

PHABSIM

'111.

0

0

Discharge

100

Fig. 5.3 Conceptualization of how PHABSTM calculates habitat values as a function of discharge. (A) First, depth(Di), velocity (Vi), cover conditions (CO, and area (Ai) are measured or simulated for a given discharge. (B)Suitability index (SI) criteria are used to weight the area of each cell for the discharge. The habitat values for
all cells in the study reach are summed to obtain a single habitat value for the discharge. The procedure isrepeated for a range of discharges to obtain the graph (C). (Adapted from Nestler et al. 1989.)
The hydraulic models have two major steps.
The first is to calculate the water surface elevation
for a specified flow, thus predicting the depth. The
second is to simulate the velocities across the crosssection. Each of these two steps can use techniques based on theory or empirical regression
techniques, depending on the circumstances. The
empirical techniques require much supporting
data; the theoretical techniques much less. Most
applications involve a mix of hydraulic sub-models to characterize a variety of hydraulic conditions at various simulated flows.
The habitat component weights each stream cellusing indices that assign a relative value between
0 and 1 for each habitat attribute (depth, velocity,
substrate material, cover), indicating how suitablethat attribute is for the life stage under consideration. These attribute indices are usually termed
habitat suitability indices and are developed using
direct observations of the attributes used mostoften by a life stage, by expert opinion about what
the life requisites are, or by a combination. Various
approaches are taken to factor assorted biases outof suitability data, but they remain indices that areused as weights of suitability. In the last step of thehabitat component, the hydraulic estimates ofdepth and velocity at different flow levels are combined with the suitability values for those attributes to weight the area of each cell at the simulated
flows. The weighted values for all cells are
summed—thus the term weighted usable area
(WUA).
There are many variations on the basic approach outlined above, with specific analyses tailored for different water management phenomena(such as hydropeaking and unique spawning habitat needs) or for special habitat needs (such as
bottom velocity instead of mean column velocity)(Milhous et al. 1989). However, the fundamentals
of hydraulic and habitat modeling remain thesame, resulting in a WUA versus discharge function (Fig. 5.3c). This function should be combinedwith water availability to develop an idea of whatlife stages are impacted by a loss or gain of available habitat at what time of the year. Time series
analysis plays this role and also factors in any

32

BIOLOGICAL REPORT 29

physical and institutional constraints on water
management so that alternatives can be evaluated(Milhous et al. 1990).
Several things must be remembered about
PHABSIM. First, it provides an index to the microhabitat availability; it is not a measure of thehabitat actually used by aquatic organisms. It can
only be used if the species under consideration
exhibit documented preferences for depth, velocity, substrate material/cover, or other predictablemicrohabitat attributes in a specific environmentof competition and predation. The typical application of PHABSIM assumes relatively steady flow
conditions, such that depths and velocities arecomparably stable for the chosen time step. PHABSIM does not predict the effects of flow on channelchange. Finally, the field data and computer analysis requirements can be relatively large.

Alternatives Analysis
The water project proponent will usually have apreferred alternative, but other alternatives mustbe identified for comparison. Other parties to thedecision process should propose their own alternatives. The alternatives analysis phase compares allalternatives with the baseline condition to facilitate an understanding of potential impacts and to
begin negotiating and creating new alternatives
more compatible with the multiple objectives of themany parties. When properly completed, simulation modeling using IFIM tools allows for straightforward comparison of many alternatives, each ofwhich is examined for
1. Effectiveness—Are the objectives of all parties
from phase one sustainable? Is no net loss ofhabitat possible on a sustainable basis? What
are the habitat costs and benefits of each alternative?
2. Physical feasibility—Do reservoirs dry up? Are
priority water rights not met? Will flooding
occur? Is enough water available?
3. Risk—How often does an alternative lead to
failure or collapse of the biological system? Is a
failure reversible? Can contingency plans be
developed?
4. Economics—What are the costs and benefits ofeach alternative?
Probably the biggest mistake the interagencygroup could make at this point is to choose one
alternative from a group of poor alternatives. It isfar better to create new alternatives, learning as

you go. When complete, this phase results in acomprehensive array of alternatives, each quantitatively described.

Problem Resolution
Given several alternatives that have been thoroughly evaluated, the choice should be obvious,
right? Usually, this is not the case; the IFIM does
not guarantee a single, best solution. The optimum
solution can rarely be identified because (1) biological and economic values are never truly commensurate, (2) data and models are never complete
or perfect, (3) rational people can reach different
conclusions, and (4) uncertainty about the future
is ever-present. IFIM was designed to aid in formulating and evaluating alternatives; however, it
still relies heavily on professional judgement byinterdisciplinary teams. The teams must integrate
their knowledge and understanding of a problem
with their professional judgements about the biological resources and social needs to reach a negotiated solution implying some kind of balanceamong conflicting social values.
The methodology is not fixed. It is open-ended
and imaginative. Flexible, mutually beneficial, negotiated solutions are encouraged (after Fisher
and Ury 1983). Negotiation is the key: (1) carefully
examine your interests and objectives before entering a negotiation, and invite criticism duringnegotiation; (2) check your assumptions about theother sides' interests; (3) focus on the problems
and each group's underlying concerns, not on theindividual negotiators or their 'positions'; (4) strive
to identify opportunities for water withdrawal or
use that maximize mutual gain; (5) insist on using
fair standards and procedures; and (6) understandthe consequences of all agreements.
We do offer one guideline for fisheries managers. When the present fishery is considered good to
excellent, the best alternative is often the one thatdeviates the least from the baseline habitat condition. This alternative is often called the 'no net lossof habitat' philosophy, which is followed by many
resource agencies. For example, no net loss ofhabitat is the official policy of the Canadian Department of Fisheries and Oceans.
Though an IFIM assessment concludes with the
Problem Resolution phase, many projects offer theopportunity for continued learning by all parties.
Because our models and judgements are by theirnature incomplete and imperfect, our predictions
are likewise incomplete and imperfect. Post-projectTHE INSTFtEAM FLOW INCREMENTAL METHOLDOLOGY 33

monitoring and evaluation, with the intent of developing into adaptive management, should be considered when appropriate. The more we understand, the better we can assess and manage thenext project. Ultimately, our goal is ensuring thepreservation or enhancement of our fish and wildlife resources.

For More Information
We are often asked for more information about
successful applications and tests of IFIM. There
have been hundreds of small IFIM applications
resulting in the incorporation of flows for sustained aquatic systems in project operations. However, they are not regularly published, nor do they
always meet everyone's definition of success. Perhaps the earliest and most completely documented
application of IFIM involved a large hydroelectric
project on the Terror River in Alaska. This application has been carefully chronicled in an information paper by Olive and Lamb (1984) and discussed
further by Lamb (1984). Another high profile successful application involved a Section 404 permiton the James River, Missouri (Cavendish and Duncan 1986). There have been niany 'scientific tests'of the methodology through the years, with varying degrees of support or refutation. The recent
paper by Nehring and Anderson (1993) is certainly
a good confirmation of the habitat bottleneck hypothesis. Another recent paper (Thomas and Bovee
1993) details the generality of some forms of habitat suitability criteria. However, the widespreaduse of IFIM by state and federal agencies (Reiser
et al. 1989; Armour and Taylor 1991) probably is
the best indicator of acceptance. Widespread use
does not imply perfection, just a lack of something
better. Additional references on IFIM and related
issues may be obtained by contacting our office (seepage iii) and asking for our publications list.

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98 pp.

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 37

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38

BIOLOGICAL REPORT 29

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82:266-273.

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 39

ATTZ The aquatic-terrestrial transition zone,
often periodically inundated and dewateredduring hydropeaking cycles.
Abiotic The nonliving, material components ofAutecology
That branch of ecology dealing
the environment, such as water, sediment, temwith interrelations between individual organperature, etc.
isms or individual species, not communities.
Acre-foot That volume of water required tocover 1 acre of land to a depth of 1 foot, equal to Backwater Generally an off-shoot from themain channel with little flow and where the43,560 cubic feet or 1,233.49 cubic meters.
water surface elevation is maintained by condiAge-class A cohort of organisms, all the sametions in the main channel acting on the downage, born within the same year. In fisheries, an
stream end of the backwater.
age group is often called Age 0, 1, 2, 3, etc. See
Baseline The conditions occurring during theYear-class.
reference timeframe, usually referring to water
Aggradation The geomorphic process in which
supply, habitat values, or population status.
inorganic materials carried downstream are deBaseline
is often some actual recent historical
posited in streambeds, floodplains, and otherperiodbut
may also represent: (1) the same cliwater bodies, resulting in a rise in bed elevation.
matological-meteorological conditions but withAnadromous Fish that mature in seawater but
present water development activities on line;
migrate to fresh water to spawn.
(2) the same climatological-meteorological conAnnual flow The total volume of water passing
ditions but with both current and proposed fua given point in 1 year. May be expressed as ature development on line; or (3) virgin or pre-devolume (such as acre-feet) but may also be exvelopment conditions. The definition of baselinepressed as an equivalent constant discharge
will always depend on the objectives of the study.
over the year, such as cfs.
Quite often, two or more baseline conditions may
Appropriation Doctrine A rule of law appliedbe necessary to evaluate a specific project.
most commonly by states west of the 100t meridian providing that the best water right accrues Bed material Mixture of substances composing
the stream's bed.
to those who first put water from a given stream
to beneficial use; characterized by the adage Biological (or fish) year Variously defined.
"first-in-time-is-first-in-right."
Often used beginning with egg deposition but
Arbitrated decision A decision made by an
may be defined as the logical start of any given
life stage or phenological relation.
objective third party. An example would be adecision in which the parties make their best Biomass The total weight of the living organcase and a third party makes the final decisionisms in some biological system at a given time.
based on the evidence. A typical arbitrated de- Biotic Of or pertaining to the living components
cision would be one made by a court.
of an ecosystem.
Area, drainage The surface area tributary to a Bottleneck See Ecological bottleneck or Habilake or stream. Sometimes called catchment
tat bottleneck.
area, watershed area, or river basin area; we Brokered decision A negotiated decision faciliprefer drainage area, which is less geographic
tated by one of the parties to a dispute. For
and has specific units (square miles).
example, a Section 404 permit would be brokered
Area, usable The area under the wetted surface
if the Army Corps of Engineers managed theof a stream that can be used by aquatic organdecision process and helped the parties reachisms. Units: square feet or square meters, usuagreement on conditions to be included in theally per specified length of stream.
permit.
Area, weighted usable (WUA) The wetted Bypass (1)A channel or conduit in or near a dam
area of a stream weighted by its suitability forthat provides a route for fish to move through or
use by aquatic organisms or recreational activaround the dam without going into the turbines.
ity. Units: square feet or square meters, usually(2) That stream reach below a dam that is essenper specified length of stream.
tially skirted by the flow used to generate electricity.
The glossary items were liberally adapted from Armantrout Carrying Capacity
The maximum number (or(nd), U.S. Fish and Wildlife Service (nd), Deason (1975),
biomass)oforganisms
of a given species that can
Norem and McCurry (1975), Schwarz et al. (1976), Milhous etbesustained
duringthat
period of least available
al. (1989, 1990), as well as from standard dictionaries.
GlOSSary2

2

40

BIOLOGICAL REPORT 29

habitat under a dynamic flow regime. Carrying
capacity should be considered a mean value fora specified, short interval (such as 1 day, 1 week,
1 month) around which populations may fluctuate.
Centrarchid A member of the sunfish family.
Channelization The mechanical alteration of anatural stream by dredging, realignment, lining, or other means to accelerate the flow ofwater.
CFS Cubic foot per second.
CMS Cubic meter per second.
Coldwater Generally, a stream populated withsalmonids.
Competition Active demand by two or moreorganisms or species for some environmental
resource in excess of the supply available.
Competitive exclusion Competition resulting
in ultimate elimination of the less effectual organism from the particular niche.
Conspecific Of the same species.
Cover Areas of shelter in a stream channel thatprovide aquatic organisms protection frompredators or a place in which to rest and conserve
energy due to a reduction in the force of thecurrent or visual isolation, such as pools, undercut banks, rock crevices, deep water, surface
turbulence, vegetation, etc.
Cross section A section across a stream channel that is perpendicular to the direction of theflow. Sometimes called a transect.
Curves, preference See Suitability curves.
Curves, Suitability-of-use SI See Suitability
curves.
Curves, usability See Suitability curves.
Cyprinid A member of the family that includes
carps and minnows.
Degradation The geomorphic process by which
streambeds and floodplains are lowered in elevation by the removal of material. The opposite
of aggradation.
Depth The vertical distance from a point on the
bed to the water surface.
Deterministic A system with fixed, specifiedstates or regular patterns.
Detritus Non-dissolved organic debris such asleaves, twigs, etc.
Dewatered A length of stream without water(for our purposes, due to human intervention).
Discharge The rate of flow, or volume of waterflowing in a given stream at a given place andwithin a given time, usually expressed as cfs orems.

Discharge, bankfull

Discharge corresponding
to the stage at which the overflow plain begins
to be flooded.
Diversion A withdrawal from a body of waterby means of a ditch, dam, pump, or other manmade contrivance.
Diversity That attribute of a biotic (or abiotic)
system specifying the richness of plant or animal species (or complexity of habitat).
Dorsal Situated near or on the back of an animal.
Drift-feeding Feeding on food items drifting in
the current.
Drought A prolonged period of less-than-average water availability.
Dry season That period of a year that is characteristically dry (and has the lowest streamflow), implying an annual seasonal cycle.
Dry year (or dry month) A time period with agiven probability of representing dry conditions;for example, a given year or month may be as dryor drier than 80% of all other similar periods.
Duration (1) The percentage of time a class of
events occurs. (2) An event's time span.
Duration analysis Examination of a certain
period of record to categorize the frequency ofclasses of events within that period, often resulting in a duration 'curve.'
Ecological bottleneck An environmental constraint resulting in mortality sufficient to substantially reduce the population size in a given
locality. Ecological bottlenecks may include
habitat bottlenecks, catastrophic floods, disease,etc.
Effective habitat (1) That portion of available
physical habitat occupied by a life stage due tomortality (or other constraint) of previous life
stages. Effective habitat analysis implies following cohorts of habitat use through time, as apopulation-limiting habitat event may not manifest itself until some later date. (2) Habitat effectively available due to hydropeaking or otherflow fluctuations reducing the habitat for a single life stage.
Effluent A discharge or emission of a liquid orgas.
Entrainment Construction of engineering
works to prevent the movement of a river, as
through dikes and other structures.
Epilimnion The upper, warmer portion of alake, separated from lower, colder portion (hypolimnion) by a thermocline.
Esocid A member of the pike family.

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY 41

Estuary The zone between the fresh water of acoastal stream and the seawater of an ocean
influenced by the tide.
Exceedence That probability of an event exceeding others in a similar class. Note that theprobability may be 'equal or exceed' or 'exceed'
only. Probabilities may also be expressed as
nonexceedence, that is, the probability of being'less than or equal' or just 'less than.'Exotic Introduced species not native to a given
area.
Firm yield That value of flow, power, or habitatthat could be maintained year-after-year despite the circumstances; for example, a reservoir's firm yield might be that amount of waterthat could be delivered to meet the demand 95%of the time for a specified planning horizon (suchas 5 years).
Flood Any flow that exceeds the bankfull capacity of a stream or channel and flows out on thefloodplain.
Floodplain That area along waterways subject
to periodic inundation by high water.
Flow (1) The movement of a stream of water orother mobile substances from place to place; (2)Discharge; (3) Total quantity carried by astream.
Flow, base (1) The sustained low flow of a
stream, usually considered groundwater inflow
to the stream channel. (2) The flow that is released during the storage phase of a peaking
cycle.
Flow duration See Duration analysis.
Flow, enhancement A flow regime that is better (in quantity or quality) than the baseline
regime for fish, wildlife, water quality, or recreation.
Flow, flushing (1) Flow of sufficient magnitude
and duration to remove fines from the interstitial spaces among the stream bottom gravel andto maintain intragravel permeability. (2) A discharge sufficient to form and maintain channel
shape and size.
Flow, mean annual The average annual volume passing a specific site. May be expressed asa mean discharge (e.g., cfs) averaged for an
entire annual period.
Flow, natural The flow regime of a stream as
it would occur under completely unregulated
conditions, that is, not subjected to regulation
by reservoirs, diversions, or other humanworks.

Flow regulated Natural flow modified by reservoirs, diversions, or other works of humans toachieve a specified purpose or objective.
Flow, steady and unsteady Flow in an open
channel is said to be steady if the depth of flow
at a single cross section does not change or canbe assumed constant over a specified interval;
the flow is unsteady if the depth changes withtime.
Fry A fish between the egg stage and the fingerling stage. Depending on the species, a fry canmeasure between a few millimeters and a few
centimeters.
Gage, stream A device for measuring the magnitude of discharge in a stream at a specificlocation.
Gradient The rate of change of any characteristic, expressed per unit of length. See Slope.
May also apply to longitudinal succession of
biological communities.
Habitat The place where an organism, or population, lives and its surroundings, both living
and nonliving; includes life requirements suchas food and shelter (see Physical Habitat).
Habitat bottleneck The cumulative constraint
on an individual species population size caused
solely by repeated reductions in habitat capacity
through time due to micro- or macro-habitat
limitations. A habitat bottleneck is a special
case of an ecological bottleneck.
Habitat capacity A limit to the maximum
number or biomass of a given species' life stage
that can exist for a specified period in a stream
reach.
Head, hydraulic The difference in elevation of
a fluid between two points.
Headwater The source for a stream in the upper tributaries of a drainage basin.
Hydrograph A graph showing the variation instage (depth) or discharge over a specified time.
Hydropeaking The practice of abruptly alternating between a low base and a high peak flow,
typically for on-peak electrical power generation; compare with hydropulsing, in which flows
may also range from low to high but are gradually varied over a longer period.
Hydroperiod The timing of significant flow
events, natural or human induced.
Hypolimnion The lower, colder portion of alake, separated from the upper, warmer portion(epilimnion) by a thermocline.
IFIM Instream Flow Incremental Methodology.

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BIOLOGICAL REPORT 29

Incremental method The process of developing an instream flow policy that incorporates
multiple or variable rules to establish, throughnegotiation, flow-window requirements or
guidelines to meet the needs of an aquatic ecosystem, given water supply or other constraints.
Usually implies the determination of a habitatdischarge relation for comparing stream flow
alternatives through time (see Standard-setting).
Instantaneous (peak) flow The single largest
flow measured instantaneously and not averaged over a longer time, such as a day or month.
Invertebrate All animals without a vertebral
column. For example, aquatic insects.
Juvenile Young of a species.
Laminar Non-turbulent, streamlined fluid flownear a solid boundary.
Larva An immature form that must passthrough one or more metamorphic changes before becoming an adult.
Lentic Standing waters, such as lakes, reservoirs, ponds, and marshes.
Life stage An arbitrary age classification of anorganism into categories related to body morphology and reproductive potential, such as
spawning, egg incubation, larva or fry, juvenile,and adult (see Cohort).
Limnology The scientific study of physical,
chemical, and biological features of inland
freshwater lakes and rivers.
Longitudinal succession Gradation in thecomposition of communities along a gradient.
Macrohabitat Abiotic habitat conditions in asegment of river controlling longitudinal distribution of aquatic organisms, usually describing
channel morphology, flow, or chemical properties or other characteristics (e.g., temperature)with respect to suitability for use by organisms.
Mainstem The main channel of a river, as opposed to tributary streams and smaller rivers
that feed into it.
Mean daily flow (1) The discharge volume
passing a given point averaged over 1 day.
(2) The average flow for 1 day computed fromseveral years' worth of data for that day. Usually expressed as cfs or cms.
Mean monthly flow (1) The discharge volume
passing a given point averaged over 1 calendar
month. (2) The average flow for 1 month computed from several years' worth of data for thatmonth. Usually expressed as cfs or cms.

Median daily flow That discharge at a given
point for which there are equal numbers ofgreater and lesser flow occurrences during
1 day.
Median monthly flow That discharge at agiven point for which there are equal numbers ofgreater and lesser flow occurrences during 1
month.
Mesohabitat Habitat types intermediate between micro- and macro-habitat (often characterized as pools, riffles, or runs) that tend tobehave similarly in response to discharge fluctuations.
Microhabitat Small localized areas within abroader habitat type used by organisms for specific purposes or events, typically described by a
combination of depth, velocity, substrate material, or cover.
Minimum flow The lowest stream flow required to protect some specified aquatic function; established by agreement or rule.
Mitigation Actions taken to compensate for actual or potential adverse effects.
Morphology The form and structure of organisms, apart from the function of those structures.
Multivoltine Having several broods in a season.
Niche The place occupied by or function of anorganism in its broad environment. May also
refer to a narrower set of habitat requirements;for example, the microhabitat niche of smaller
fish is in slower, shallower water.
Open channel hydraulics The analysis ofwater flow and associated materials in an open
channel with a free water surface, as opposed toa tunnel or pipeline.
Operation rule Criteria by which managers ofwater projects decide when and how muchwater to store, release, or divert.
Palustrine Living in a marsh or swamp environment.
Periodicity That pattern or timing during a biological year when a given organism or life stage
is active or present in the system under study.
Persistence A nonrandom process within atime series of hydrological or meteorologicalevents that tend to have high events following
other highs and low events following otherlows.
PHABSIM (pronounced P-HAB-SIM) The
Physical HABitat SIMulation system; a set ofsoftware and methods that allows the computation of a relation between stream flow andTHE INSTREAM FLOW INCREMENTAL METHOLDOLOGY

physical habitat for various life stages of anaquatic organism or a recreational activity.
Phenology The periodic natural patterns ofmaturation, timing, or distribution in the life
history of an organism.
Phenotype Visible characteristics of an organism.
Physical habitat Those abiotic factors (suchas depth, velocity, substrate material, cover,temperature, water quality) that make up someof an organism's living space (see Habitat).
Phytoplankton Plants drifting with the surrounding water.
Piscivorous Feeding on fishes.
Pool Part of a stream with reduced velocity,
often with water deeper than the surrounding
areas, which is usable by fish for resting andcover.
Preference curves See Suitability curves.
Q7-10 The lowest continuous 7-day flow with a
10-year recurrence interval. Sometimes called
7Q10.
Ramping

43

Segment

Relatively homogeneous section of a
stream composed of one or more reaches (homogeneity usually refers to at least the channel
morphology and discharge within that segment). Boundaries are placed wherever the
stream undergoes a significant change in discharge, channel structure, water quality, or
temperature, usually at tributary confluences
and at major diversions. Usually considerably
longer than 10-14 times the channel width.
Segment length The length (in miles or kilometers) of a reach of stream for which relatively
homogeneous conditions exist, allowing characterization of habitat versus flow by a single relation.
Slope The inclination or gradient from the horizontal of a line or surface. The degree of inclination can be expressed as a ratio, such as 1:25,
indicating one unit rise in 25 units of horizontal
distance or as 0.04 length per length. Sometimes also expressed as feet per mile.
Spawn To lay eggs, especially of fish.
Stage The elevation or vertical distance of thewater surface above a datum or reference (aplane of known or arbitrary elevation).
Standard-setting (1) A stream flow policy or
technique that uses a single, fixed rule to establish (minimum) flow requirements despite dynamic aquatic ecosystem needs. (2) The processof determining minimum flow requirements fora water project or water right. The minimum
flow may, to varying degrees, consider genericecosystem needs (see Incremental Method).
Standing crop Quantity of living organisms
present in the environment at a given time.
Often refers to the harvestable portion of a
population.
Steady flow See Flow, steady and unsteady.
Stochastic Allowing for randomness or variability in processes. Literally, making a best
guess.
Stream width See Width, stream.
Streambed The bottom of the stream channel;
may be wet or dry.
Substrate The material on the bottom of thestream channel, such as rocks or vegetation.
Suitability curves or indices Collectively refers to category one to four suitability index (SI)curves (see next four entries).

The rate of change in discharge at acontrolled release for hydropower purposes.
Reach A comparatively short length of a
stream, channel, or shore. One or more reaches
compose a segment. The actual length is definedby the purpose of the study but is usually nogreater than 5-7 times the channel width.
Reach length The length of a section or piece ofa river.
Recurrence interval The inverse of the probability that a certain event will occur, normally
expressed in years. For example, a flow with arecurrence interval of 10 years would be expected to occur, on average, once every 10 years.
Redd A fish nest typically dug in a river or lake.
Regime The general pattern (magnitude andfrequency) of flow or temperature events
through time at a particular location, (such as,snowmelt regime, rainfall regime).
Riffle Shallow rapids in an open stream wherea turbulent water surface is induced by obstructions wholly or partly submerged.
Riparian On or by a water supply, such as near
the water's edge.
Rule curve See Operation rule.
Salmonid A member of the family that includes
salmons, trouts, chars, and whitefishes.
Suitability curves—Category one or literaSediment Solid material, both mineral and orture-based The first category of curves, based
ganic, that is in suspension in the current or
on available speculative information, including
deposited on the stream bed.
literature sources and expert opinions; usually

44

BIOLOGICAL REPORT 29

concerns a species response to a macrohabitat
variable.
Suitability curves—Category two or utilization A curve based on frequency analysis offish observations in the stream environment.
Suitability curves—Category three or preference A utilization curve that has been corrected for environmental bias; for example, if
50% of fish are found in pools over 1.0 m deep,
but only 10% of the stream has these pools, thefish are actively selecting that habitat type.
Suitability curves—Category four or conditional A preference curve that is conditioned(stratified) by cover, season, or another subdivision.
Synthetic hydrograph A flow time series artificially constructed for a given location throughvarious analytical techniques.
Time series A record of events (flow, habitat, orother) through time; usually describes those
events for a regular averaging interval, such ashours, days, weeks, months, or years.
Time series analysis Analysis of the pattern(frequency, duration, magnitude, and time) of
time-varying events. These events may be discharge, habitat areas, stream temperature,
population factors, economic indicators, power
generation, and so forth.
Total habitat Total available wetted area conditioned by microhabitat and macrohabitat suitability and summed for all relevant river segments.
Transect See Cross section.
TSLIB A set of computer programs and analytic
methods useful for performing time series
analysis.
Turbidity A measure of the extent to whichlight passing through water is reduced due tosuspended materials.
Uniform flow See Flow, uniform and varied.
Unsteady flow See Flow, steady and unsteady.
Usable area See Area, usable.
Utilization curves See Suitability curves.
Varied flow See Flow, uniform and varied.
Velocity The time rate of motion; the distancetraveled divided by the time required to travelthat distance.

Velocity, adjacent A velocity in a cell near thecell being considered.
Velocity, mean column The velocity averaged
from the top to the bottom of a stream.
Velocity, nose The velocity at the point wherea fish is located. This is point velocity expressedin terms of an organism.
Warmwater fishery Generally, an aquatic environment too warm for salmonids.
Water budget (1) The balance of all water moving into and out of a specified area in a specified
period. (2) An administratively segregated volume of water reserved for a specific use.
Water right A legally protected right to divert
or store water for beneficial use.
Water surface elevation (WSL) The elevationof the water's surface in relation to an arbitrary
datum.
Water year 1 October through 30 September;usually considered representing the annual hydrologic cycle beginning with that period of consistently low flows.
Weighted usable area (WUA) See Area,
weighted usable.
Wet season That period of a year that is characteristically wet (and having the greatest stream
flows), implying an annual seasonal cycle.
Wetted perimeter The distance across the bottom and sides of a channel cross section, perpendicular to the flow, in contact with water.
Roughly equal to the width plus twice the mean
depth.
Wetted width See Width, wetted.
Wet year A water year characterized by above
average discharge. Exact measure of deviationfrom some average or median value depends onthe decision setting.
Width The distance across a channel at the0water surface measured normal (90 ) to flow.
Width, stream Either the same as the channel
width or the width of the wetted stream.
Width, wetted The width of the stream withwater in it.
Year-class A cohort of organisms born within a
specified calendar year (such as the 1986 yearclass; see Age-class).

THE INSTREAM FLOW INCREMENTAL METHOLDOLOGY

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