Grand Canyon Monitoring and 

Research Center Monitoring & 

Research Plan to Support the Glen 

Canyon Dam Adaptive Management 

Program: 2007-2011

Developed in cooperation with the Glen Canyon Dam 

Adaptive Management Program 

Draft version: November 21, 2005 

Southwest Biological Science Center 

2255 Gemini Drive, Flagstaff AZ 86001

 
11/07/05 - Revised Draft MRP Sentence Outline – New Edits - 11/20/05 

GCMRC INTEGRATED MONITORING AND RESEARCH PLAN 

FY 2007-2011 

IN COOPERATION WITH GCD AMP 

CHAPTER 1. THE GCD AMP STRATEGY FOR SCIENCE PLANNING 

 

A. The AMWG, GCMRC and TWG propose a more comprehensive and 

responsive approach to science and management planning that incorporates all 

active GCD AMP groups, including Ad Hoc Groups. The new science 

planning process incorporates both strategic planning for 3-5 years and 

operational and budget planning at two year intervals. 

B. The New Science Planning Approach Develops a More Holistic and 

Adaptive Science and Management Planning Process 

1. Incorporating all GCD AMP Groups in the planning process, i.e., GCMRC, 

TWG, Ad Hocs, SAs, AMWG, external science and management, desired 

 community. 

 2. Incorporating operating adaptive management principles in the planning 

process, i.e., rapid cycling of science and management trails new knowledge 

and management application within a 5-year period. 

3. Applying more ecosystem based science processes, including ecosystem

modeling and assessment approaches. 

4. Annual evaluations of potential new knowledge application and management 

actions. Complete management and program assessments of potential 

science management changes at 3-5 year intervals and requirements for new 

or additional science. 

CHAPTER 2: THE PURPOSE AND DIRECTION OF GCMRC RESEARCH AND 

MONITORING PROGRAMS 

A. GCMRC’s Research and Monitoring Purpose: To provide credible, 

objective research and monitoring information to the GCD-AMP 

1. Critical needs for increased knowledge exists in experimentation to 

determine the most appropriate flows, and other management actions 

such as selective withdrawal to maintain or improve CRE Resource; in 

research studies and modeling to establish better understanding of 

resource integration and linkages; and in studies to develop improved 

monitoring protocols or new monitoring procedures. 

2. The GCD AMP (including the GCMRC) are established to evaluate and 

recommend differing GCD operations that maintain and/or improve the 

resources for which Grand Canyon National Park was established to 

protect. This is accomplished through managed actions for protection of 

 
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these resources. Critical to taking these managed actions and 

understanding their impacts are ongoing research and monitoring 

programs. 

3. The GCD future operations were fully evaluated in the EIS (DOI, 1995), 

and new operating procedures specified in the established ROD (DOI, 

1996). As presented in the GCD-AMP strategic plan, the ROD specifies 

that: 

a. An adaptive management program be developed to implement the 

 ROD and requirements of the GCPA. 

b. A science center is established to develop the required research 

 and monitoring to best inform management decision processes in 

 development of new ecosystem science understanding of the 

 resources of the CRE. 

4. The GCMRC develops science approaches (research and monitoring) for 

prioritized goals of the AMWG (GCD-AMP). Primary shifts in emphasis 

occur over decadal periods. Current emphasis exists with endangered fish

(HBC), sand and campable beaches, cultural resources and water quality. 

Within general goals, i.e., endangered fish, such as HBC, several major 

emphasis areas may be identified for 3-5 year program periods. For 

example, the issue of low HBC recruitment has resulted in intense multiyear research and modeling programs to determine food base, water 

quality and predation impacts. 

5. The overarching mission of the GCPA and GCD-AMP is to maintain or

improve the condition of critical CRE resources such as native fishes, 

cultural resources, sand beaches, etc. 

B. Conducting Structured Science for the GCD AMP 

The ROD is specific in identifying science approaches to be pursued in the GCDAMP, especially as relates to specification of goals and information needs for 

science; application of an adaptive management program approach; pursuing an 

integrated ecosystem science paradigm; and directing all science activity at 

improving CRE resource knowledge: 

1. Adaptive management is a critical tool for managers who work with 

natural and cultural resources. Introduced in the 1970s by Holling (1975, 

1978), it is now applied across all agencies of USDOI. Its application 

requires adherence to three principles. 

a. That resource management can be advanced rapidly 

 and effectively through close working relationship of managers 

 and scientists. 

b. That scientists respond to information needs of managers rapidly 

with contributions of applied experiments, research and 

 monitoring. 

c. That managers apply new knowledge quickly as available and 

evaluate and monitor with science needed corrections in 

management actions. 

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2. The adaptive management process implemented in the GCD-AMP 

requires managers to continually inform science regarding several factors. 

 These factors include: changes in information needs, and priorities; 

changes in desired future resource conditions, and level of resolution 

needed in data/information. A process will be developed to specify 

desired future conditions for CRE resources. 

3. The GCMRC must provide a continual stream of integrated information 

to managers from research and monitoring programs. The provided 

science must address manager needs and issues related to the resources 

from an ecosystem perspective, providing both an understanding of key 

linkages in the system, but also the interacting requirements of processes 

and resources in the total system. 

C. Integrated Research and Monitoring Approaches to Respond to 

Management Issues and Resources of Concern 

1. Research and monitoring activities are the primary science drivers for 

GCMRC. The research program incorporates three primary thrusts;

experimentation, research to improve science and management 

understanding, and studies to develop new monitoring protocols or 

improve current methods. The scope of the research program is extensive, 

constantly developing new science knowledge in the above three research 

programs, and for nine major resources, i.e., native fish, cultural, water 

quality, etc. 

2. Monitoring includes data collection across all resources of concern for 

differing resource parameters and with differing time and space 

dependencies, and levels of resolution. Most monitoring projects are 

considered core to the overall science program, and will be given priority 

in the overall science planning and budgeting process. However, even 

these science efforts may be revisited in the budget planning process. 

3. Goals and information needs are contributed through resource managers 

and stakeholders. They are also prioritized to assist science and 

management planning. Managers will define desired future resource 

conditions, key project parameters, data resolution required, etc. 

4. Resources of concern are identified primarily through a merging of the 

goal prioritization process and the science knowledge assessment process. 

Over the last decade the primary resources of concern have been 

somewhat consistent. Native fish, cultural resources, sediment and 

beaches, and aquatic food and water quality, have continued as key 

resources to most managers and stakeholders. Following is a listing of 

goals developed by managers: 

• Fish and Aquatic: Native fish especially humpback chub; non-native 

rainbow trout in the Lees Ferry reach; and aquatic food base. 

• Cultural Resources: Register eligible historic properties, tribal

concerns. 

• Sediment: substrate, beaches, sediment storage 

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• Threatened and endangered species: Humpback chub, Kanab 

ambersnail, Southwest willow flycatcher. 

• Vegetation: terrestrial wildlife, exotic and invasive species. 

• Water: hydrology, springs, riparian habitat, water temperature, water 

quality, flow dynamics, TCD. 

• Hydropower: power capacity, energy generation. 

• Recreation: quality of recreation experience, recreational boating, 

fishing, socioeconomic benefits. 

• Adaptive management process, ecosystem management, integrated 

research. 

D. A Historical Chronology of CRE Research and Monitoring Programs; 1950-

2006 

Observation and study of the CRE was initiated by Powell as part of his general 

physical (1878), biotic, and ethnic resource assessments of the southwest. This 

effort has been extended by intermittent studies up to 1950 and has several 

primary areas as follows.

1. Phase 0 - 1950-1982: During this period several organized investigations

took place. None were continuous over the period, and were initiated for 

differing reasons. They included BOR, Dartmouth, NPS and AGFD, as 

well as others. 

2. Phase I - 1982-1988: “GCES Phase I”, was initial BOR science program 

to determine whether or not dam operations were affecting downstream

resources. Challenge: Determine whether or not dam operations were 

influencing downstream resources with respect to peaking power flows. 

Establish methods for science programming in CRE, establish baselines. 

3. Phase II - 1989-1995: “GCES Phase II” was advanced program to 

establish active science studies tied to GCD releases (1990) & 

implementation of interim flows (1991); morphed into the EIS. Passage 

of GCDA (1992) and GCD EIS (DOI, 1995). Challenge: In cooperation 

with senior ecologist, establish status of knowledge on critical resources 

and define best management practices, improve baseline information and 

develop a monitoring program that promoted integrated science. 

Completion of the EIS become the primary focus of this era. 

4. Phase III - 1996-2000: “Transition Monitoring” era during which time 

GCMRC/AMWG programs of adaptive management and ecosystem

science were formerly established. Evaluate designed management 

actions (flows) on key resources using adaptive management. 

Challenges: Development of a conceptual ecosystem model and 

determine protocols for use of effective adaptive management, 

developing ecosystem science procedures, assuring quality science. 

5. Phase IV - 2001-2006: GCMRC/AMWG/TWG/BAHG/SA. Both the 

AMWG and GCMRC strategic management plans are developed and 

implementation of Active Adaptive Management is underway in 2003 

with large-scale flow and non-flow experimental treatments. Based on 

improved science knowledge of resource impacts of management actions, 

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revised management policies are incorporated as experiments, monitoring 

and management actions for 2007-2011. Challenges: Continued support 

of research & development of monitoring protocols for major resources 

tied to GCD AMP Goals, while also conducting focused experimental and 

non-experimental research. Assuring science leadership and productivity, 

improving ecosystem science implementation, improving adaptive 

management process, focus limited resources in key resource needs. FY 

2006 is milestone year for assessing new level of knowledge acquired 

through experimental approaches and basic research. This information is 

incorporated into strategic science planning that charts the activities of 

the Center for the next 5-10 years. 

6. Phase V - 2007-2011: GCMRC/AMWG/TWG/BAHG/HBCCP/SPG/SA. 

Challenge: The next phase of GCD AMP programs must improve the 

Adaptive Ecosystem Management process and incorporate more effective 

ecosystem science approaches, including active experimental studies, 

monitoring, and developing collaborative science partnerships. 

Significant advances in science and management knowledge is necessary 

to develop improved management actions for stabilizing HBC population 

and long term sand depletion in the CRE. The next phase for ecosystemscale conceptual modeling is proposed as a means of advancing synthesis 

of knowledge in a more integrated setting. 

E. Research and Monitoring Strategies that will Improve Implementation of 

Ecosystem Science in the GCD-AMP

 1. Expanded design, development and use of a conceptual ecosystem model. 

In FY 2006-2008 upgrade the Colorado River Socio-Ecosystem Model. 

Possible additions are: 

a. Capture social system components not currently captured in 

the model and improve information for adaptive 

management and agency decision processes 

b. Moving to landscape scale; i.e., linking Lake Powell, LCR, 

Paria to CRE and include additional terrestrial components 

c. Additional fishery elements (cold and warm water fish 

predation on HBC, Pathogen impacts on HBC, etc.) 

d. Modeling to predict outcomes of non-flow management 

 activities (mechanical removal of non-natives, native fish 

refugia or grow-out programs, check dams, translocation 

efforts for HBC, tributary triggers for sand, fine-sediment 

 augmentation, etc.) 

e. Terrestrial vegetation changes 

f. Coupled Lake Powell and downstream temperature simulations 

linked to fine-sediment, food web and fisheries sub-models 

g. Enhanced use of climatic input data and simulations 

h. Recreational use and campsite size/abundance/distribution 

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i. Cultural resource change and protection strategies 

j. Financial impact simulations coupled to operation flow submodels 

2. Explicit science project design of system data components that 

specifically address the overarching science questions and promote 

integration and linkage to other system components. (examples: recent 

solicitations for the food web research). 

a. Explicit design of science projects that specifies linkages across 

projects and integration of programs to a landscape level. 

Promote integration at level of solicitation and proposal 

development, while also maintaining focus on conceptual 

modeling paradigm and previous accomplishments (1998-2001). 

b. Incorporation of “looking outward” ecosystem matrix links 

(Holling, 1978) to fully characterize effectors and impacts of 

processes relating various resources and processes. Tie 

management actions and desired outcomes directly to conceptual 

modeling and strategic science activities in Research Center. 

3. Analysis of data and evaluation of research and monitoring information from

an ecosystem perspective. 

a. Incorporating conceptual, simulation and/or predictive ecosystem

sub-models to formulate and define critical processes/and 

integration of resources to enhance data analysis and evaluation 

of resource impact associations. Focus on synthesis and 

integration of new and historic data. 

b. The use of linked physical sub-models that define how flow and 

fine-sediment export relates to cultural resource site erosion 

throughout the river corridor. 

c. Flow and sediment simulations designed to evaluate optimized 

strategies for implementation of Beach/Habitat-Building Flows. 

Concepts of linear programming developed as part of 

prescription for achieving sediment objectives linked to longterm monitoring of sediment and habitats. 

4. Assessment of science and management interactions in adaptive management 

from a system perspective. 

a. CRE systems model for adaptive management and decision 

processes designed and linked to the more objective ecosystem 

science process. 

F. Using information needs, knowledge assessments and ecosystem models to 

enhance conceptual model effectiveness in identifying knowledge gaps and 

 science needs. 

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1. Matrix assessments of system information needs across physical, biological, 

socio-cultural resources, strategically using knowledge assessments 

(milestone) stakeholders needs, and model evaluations to link learning with 

planning of science activities. 

2. Using Science Questions to Guide the Research and Monitoring Process 

a. The research and monitoring programs will be structured around 

overarching science questions and other questions that refine the 

inquiry. 

b. These questions capture the ongoing priority goals and 

information needs of managers and stakeholders. 

CHAPTER 3. DESIGNING A RESEARCH PROGRAM TO RESOLVE 

MANAGEMENT ISSUES AND ECOSYSTEM SCIENCE QUESTIONS 

The new GCMRC science program is organized around issues, goals, and information 

needs of managers and stakeholders. Implementation of science efforts are within an 

adaptive management process, and will use an ecosystem science paradigm driven by 

fundamental science questions. Experimental designs used, and research and monitoring 

projects implemented are structured to respond directly to overarching and refined 

questions for each goal. 

A. Development of Overarching and Refined Science Questions to Respond to 

Gaps in Management Information Needs and Guide the Science Inquiry Process

1. The GCD-AMP process is driven by managers specifying priority goals and 

information needs, many of which can be addressed by GCMRC specifying 

explicit questions to guide research and/or monitoring programs/projects. 

2. The GCD-AMP’s AMWG has specified the following general goal areas 

with greatest priority assigned to endangered fish, aquatic, cultural, and sand 

resources. 

• Fish and aquatic 

• Cultural resources 

• Sediment, with emphasis on sand 

• T&E species 

• Vegetation 

• Water

• Power 

• Recreation 

• Adaptive process and science 

3. Within each goal AMWG has specified several information needs that are 

expressed as either Research Information Needs (RINS) or Core Monitoring 

Information Needs (CMINS). Generally, it is expected that CMINS would 

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be satisfied through a monitoring program, and likewise for RINS through a 

research program. 

4. Formal knowledge assessment processes by GCMRC and CMIN and RIN 

assessments and Science Planning by GCD AMP/GCMRC in FY 2006 

identified knowledge gaps in the CMINS and RINS that are satisfied by 

GCMRC developed overarching and refined science questions. An overall 

assessment of these knowledge gaps is provided in Figure 3.1. 

5. An example of the linkage of goals and information needs to science 

 questions and research and monitoring projects is displayed in the 

 following hierarchical linkage of science to the goal of aquatic food base. 

AMWG Goal: Protect or improve the aquatic food base so that it will 

support viable populations of desired species at higher trophic levels. 

 

AMWG Information Need: Identify the contribution of primary and 

secondary productivity to the aquatic food web, and identify how 

operations affect productivity and food web dynamics. 

GCMRC overarching science question. What are the primary food 

base components and their relative contributions to the aquatic food 

web?

 

GCMRC refined research question. 

• What are the important pathways, and the rate of flux among 

them that link lower trophic levels with fish? 

• How is invertebrate flux affected by water quality and dam

operation?

• Are trends in the abundance of fish populations or indicators 

associated with fish, correlated with patterns of food availability 

and/or quality?

• What is the most effective monitoring approach to reflect the 

information needs for the AMP? 

GCMRC Monitoring Project. Aquatic food web monitoring (Tied to 

CMINS that may be subject to revision) 

This portion of the program is under development but may include: 

• Bioenergetics modeling 

• Whole river metabolism 

• Secondary producer monitoring 

• Fish diet sampling 

• Utilization of fish abundance data from fisheries monitoring.

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Figure 3.1. Conceptual portrayal of general some of the information gaps identified 

through GCMRC knowledge assessment

Resource 

Objectives 

Restore 

Sand 

Habitats & 

Warm River 

to Increase 

Native 

Fish 

Warmer

Dam

Releases 

From

(Naturally

or from 

A Control 

Device) 

Changing

Annual 

Monthly 

Release 

Pattern 

(Lower 

Seasonally 

Adjusted 

Daily Peaks) 

Artificial 

Floods to 

Restore 

Habitats 

(After 

Sediment 

Inputs from

Downstream

Tributaries)

Increased 

Daily 

Fluctuating 

Flows 

(Following 

Peak 

Energy 

Demand)

Sustained 

Low 

Steady 

Flow 

(Below 

Average 

Condition) 

Sustained 

High 

Steady 

Flow 

(Above 

Average 

Condition) 

Physical 

Removal 

of NonNatives, 

(Cold 

Water 

Species 

Of Fishes) 

Physical 

Removal 

of NonNatives, 

(Warm

Water 

Species 

Of Fishes) 

Increase

Sand in the 

River 

(+) (+) (+) 

(-) 

(+) 

(-) 

N/A N/A 

Promote

Backwater 

Habitats 

(+) (+) (+) 

(-) 

(+) 

(-) 

N/A N/A 

Support

Native Fish 

Recruitment 

(+) (+) 

(-) 

Limit

Non-Native 

Fishes 

(+) (+) (+) 

Increase 

Near-shore 

Temps. 

(+) (+) 

(-) (-) 

(+) 

(-) 

N/A N/A 

More 

Stable

Shorelines N/A 

(+)

N/A 

(-) 

(+) (+)

N/A N/A 

Benefit to 

Hydropower

(-) (-) (-) 

(+)

(-) (-) N/A N/A 

TABLE EXPLANATION: Example of simplified Uncertainty Matrix for Colorado River 

Ecosystem in Grand Canyon, USA. The table depicts levels of knowledge about the flow (dam

operations) and non-flow treatments with respect to some key river resources of concern, such as 

hydropower, endangered, native fish and physical habitats. Notes: 1) (+), positive response 

predicted relative to management objective; (o), neutral response; (-), negative response, N/A, 

not applicable, 2) responses assume dam operations are constrained by fixed monthly volumes,

3) suite of operational elements are contained within column “Increased Daily Fluctuating 

Flow,” such as hourly ramp rate, flow range, peak, minimum flow, for any given monthly

volume release, relative to the operational policy implemented in 1996 for the dam. Shading: 

White – scientists can predict the direction and the magnitude of resource response relative to 

flow or non-flow treatment, Gray – Owing to unresolved uncertainties, scientists can predict the 

direction, but not the magnitude of response, Black – Uncertainties are so large that a link with 

dam operations is suspected, but too little is known to make a prediction for resource response 

direction or magnitude of response.

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6. The linkage of goals, information needs, over-arching and refined 

science questions and monitoring approaches is developed in the 

conceptual ecosystem model. The resources of concern are tracked 

through monitoring and/or research studies. For the aquatic food base, 

identifying the important pathways and how the components fluctuate 

under operations is a key information need for Goals 2 and 4 and 

supports recreational goals associated with angler satisfaction. This 

effort represents a research element. Once these pathways and 

components are better understood, monitoring of changes in attributes of 

the food base and fish abundance and condition can more clearly be 

related to operations. 

B. Research Program Elements 

 The research program is divided into three research categories: 

1. Experimental program

2. Required research to ensure management and science understanding of 

resources and resource interaction, including advanced conceptual 

modeling 

3. Required research to develop and/or improve monitoring protocols, 

procedures, effectiveness 

C. Ecosystem context of Research Program Over Planning Period 

1. Explicit and implicit research and monitoring outcomes needed and 

 associated requirements on research. 

2. The dependence, linkage and integration of science (research, 

monitoring) and contribution of research 

3. Projected management actions and associated research needs.

D. Relating Status of Knowledge to Research Information Needs, Uncertainty, 

Knowledge Gaps and Research Questions 

1. Periodic assessment and evaluation of knowledge is a requisite for 

identifying and focusing monitoring and research directions that address 

information needs of managers. Assessments are applicable to both 

monitoring and research approaches and included Protocol Evaluation 

Panels, Knowledge Assessment Workshops, and data synthesis reports. The 

interval between reviews is approximately 5 years, and should coincide with 

strategic planning and experimentation. 

 

2. Knowledge gaps exist among many resources in the CRE with some being 

fundamental to our understanding of how to manage the resource (e.g., 

recruitment bottlenecks associated with life stages of humpback chub). 

System-wide treatment blocks, mini-experiments and off-site lab 

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experiments can be employed to resolve cause and affect relationships. 

Examples include 

• Mechanical removal – removal efficacy and predation/competition 

question. 

• High Test Flow following sediment input triggers – possibility of 

managing and conserving sediment resources. 

• Translocation of HBC – evaluating possibility of expanding HBC 

range. 

3. Assessment and review is also pertinent to monitoring programs. Review of 

the adequacy of monitoring information may result in reconsidering how and 

what data are collected for a resource. Research to improve data collection 

methods or to better define what data should be collected is another aspect of 

the research program. Project in that past that were research for the purpose 

of developing monitoring include: 

• Sediment transport and mass balance project 

• Lees Ferry trout monitoring 

• Terrestrial ecosystem monitoring 

• Cultural resource monitoring 

E. Designing an Appropriate Experimental Program to Address Resource 

Effects of Management Actions and Treatments

1. Selecting appropriate experimental program design and expected analysis 

capabilities – embracing the concept of a “Hybrid” design. There is a critical 

need to clearly identify management goals and objectives with regard to 

tangible resource outcomes. Are the desired outcomes of the GCD-AMP 

both Measurable & Attainable? Example: Mechanical Removal - methods 

developed during 2003-2005 research are known to reduce the abundance 

and distribution of exotic, coldwater species within treatment reaches in 

Marble & Grand Canyons and the reduced abundance can apparently be 

maintained through continued implementation. Is this currently a stated 

Management Objective? 

 

There is also a need to define the level of science support required from

GCMRC for environmental compliance, as well as the protocols for how the 

ROD is amended. For experimental treatments to become management 

actions, decision makers would presumably need to modify the Record-ofDecision, but only following fulfillment of compliance requirements. 

a. Pursuing an Appropriate Design - following process of dialogue between 

managers and scientists that effectively identifies which actions are 

understood well enough to be treated as long-term management actions if 

appropriate (in pursuit of the so called “hybrid design” experimental design), 

AMWG forwards recommendations to the Secretary of DOI to consider as 

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amendments for revision of the ROD, pending legal compliance 

requirements. 

b. Experimental design is then pursued which will effectively evaluate 

uncertainties about the effects of remaining experimental policies on key 

resources in CRE (presumably, the other management actions which were 

not included in recommendations for long-term implementation as revisions 

within the ROD). 

c. Review the strategic science questions derived from ongoing knowledge 

assessments that would need to be addressed to reduce uncertainties related 

to the proposed experimental policies tied to the GCD-AMP Strategic Plan. 

d. Identify additional modeling, non-experiment research & monitoring and 

specific flow and non-flow elements within the agreed upon experimental 

design (including short-term field studies, for example, related to sand bar 

dynamics) that are required to answer the strategic science questions to meet 

management needs. 

e. Compare and evaluate the experimental policies with respect to the stated 

management goals vs. costs and benefits. 

2. Specifying management actions and treatments 

The key science questions drive the experimental actions and treatments 

(flow and non-flow) that focus the experimental policies to be tested, for 

example, those related to the USFWS 1994 Biological Opinion and its 

Reasonable and Prudent Alternatives. On that basis, issues related to both 

the thermal regime and the stability of shoreline rearing habitat are relevant 

with respect to the following questions: 

• What ultimately limits native fish populations: 

 production of young fish from tributaries 

 spawning and incubation in the mainstem

 survival of YoY and juvenile stages in the mainstem

 growth and maturation in the adult population as influenced by 

mainstem conditions? 

• What is the relative importance of increased water temperature, shoreline

stability, food availability, and predators on the survival of early life 

stages of native fish?

• How important are backwaters and vegetated shoreline habitats to the 

overall growth and survival of YoY and juvenile native fish? 

• Do the potential benefits of improved rearing habitat outweigh negative 

impacts owing to increases in non-native fish abundance or disease?

Policies to be experimentally evaluated would likely include, but not be 

limited to: 1) construction, implementation and rigorous evaluation of a 

Selective Withdrawal Structure (SWS) at GCD and 2) studies on the early 

life history of humpback chub with respect to recruitment related to 

fluctuating versus stable flow operations from GCD. In addition, studies 

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focused on removal of exotic fishes could address the role of predation and 

competition with natives. Finally, the role of sand bar related habitats in the 

near-shore environment (recruitment success of YoY native fish relative to 

abundance and distribution of backwater) as related to early life history 

success of native fishes.

3. Maximizing abilities to determine effects and minimizing confounding 

variables 

4. Options for modifying the experimental design owing to changes in natural 

phenomenon (climatic forced swings in basin hydrology, tributary sediment 

production, etc.) 

F. A Proposed FY 2007-2011 Experimental Program 

 

1. Specifying key science questions 

2. Assessment of management action(s): at present, only MLFF (w/ occasional 

BHBF’s and HMF’s) constitutes the Record-of-Decision 

Continue process of ongoing dialogue between managers and scientists 

regarding MLFF We know that stable flows that are “low” (less than 10,000 

cfs range) are most effective at conserving sand, amplifying warming 

downstream and stabilizing near-shore habitats. Short-duration BHBF-type 

releases (2-4 days at 41,000-45,000 cfs)) can mobilize sand from the lower 

channel and deeper eddies and deposit this material to higher elevation 

shorelines relatively quickly when sand supply is enriched. The MLFF has 

likely improved some aspects of the recreational rafting and camping 

experience, as well as angling, but there no data on this (SCORE). We do 

know that under MLFF, campable area above the 25,000 cubic feet per 

second flow line has decreased, while campable area below the 25,000 flow 

level has increased. (Kaplinski and others, 2005). 

3. Design options, strengths, and limitations 

Several design options can be considered for the experimental approach, 

including forward and reverse titration or a factorial design (Figure 3.2.) 

a. Natural warming; surrogate for Selective Withdrawal Structure 

(SWS) 

b. Mechanical removal (both cold and warm fishes) 

In fact, we have 15 years of a forward titration design already behind us with 

pretty solid data for both sediment and fisheries (Figure 3.3). The MLFF 

(and its precursor, Interim Operation) was implemented from 1991 through 

2001 with no Mechanical Removal or persistent thermal warming event. 

Then, we continued mostly MLFF operations and implemented MR along 

with nature’s own version of the Selective Withdrawal Structure (SWS) 

since 2002. Hence, after an 11-year long “block” of MLFF with cold water 

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and unconstrained RBT recruitment, we are now heading into the 4th year of 

a block of MR coupled with a warm main-channel “event” conditions. 

Selective Withdrawal Structure decision point needs to seek resolution in

2006, while pursuing research related to monitoring and control of warm & 

cold fish species in downstream reaches of interest relative to native fish 

monitoring and research questions, as well as management goals. 

MLFF Under the Range of Upper Basin Hydrologic Cycle If we continue 

monitoring the MLFF under the paired implementation of MR and warming, 

we have no way of ensuring that warming will continue. 

Managers might choose to enhance the probability of a HBC recruitment 

signal by recommending stable fall flows, but that could confound ability to 

discern MR & temperature from habitat stability. 

4. Proposed assessments 

-Ongoing evaluation and refinement of Mechanical Removal (relative to 

influence on HBC recruitment success), 

-Ongoing evaluation of BHBF concept (under enriched conditions) with

respect to sustainable, long-term flow prescription (using field studies and 

modeling simulations), 

-Full evaluation of thermal regime relative to biological responses under 

SWS warmer conditions (including, development and calibration of 

downstream thermal simulations using monitoring data). 

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Figure 3.2 Pros and Cons of Block and Titration Designs 

BLOCK DESIGN 

PROS 

• Long timeframe

• Partitions variance 

• Increased learning 

• Cause and effect

CONS 

• Long time frame

• Emphasizes learning 

• Long-term commitment 

TITRATION DESIGN 

 PROS • Implements management actions 

• Improves some knowledge 

CONS 

• Decreased learning

• Cause and effect not identified (specific actions

• Confounding factors

• Not a recognized design

• Analysis methods uncertain (e.g., main effects vs. interactions)

 

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Figure 3.3 Status of Evolved Factorial Design on Basis of Historical Perspective 

Status of Evolved Design on Basis of Historical Perspective

IMPLEMENT TREATMENT TREATMENT NOT IMPLEMENTED

???(No BHBF) ML Experimental Fish Removal ??? FF+Fall Testing *WY2006, decision

[?,?]

[+,+](W/ BHBF) MLFF+EXP FF+Fall Experimental Fish Removal [++,++] Testing

WY2005, [?,?]

WY2004, [?,0] MLFF+EXP FF Experimental Fish Removal [+,+] [-,-](No BHBF)

WY2003, [?,-] MLFF+EXP FF Experimental Fish Removal [+,+] [-,-](No BHBF)

WY2002, [?,-] MLFF only No Exotic Control [0,0] [-,-](No BHBF)

WY2001, [?,+] MLFF only No Exotic Control [0,0] [+,-](No BHBF)

WY2000, [+,+] MLFF+LSSF+HMF No Exotic Control [0,+] [-,-](No BHBF)

WY1999, [+,+] MLFF only No Exotic Control [0,0] [+,- (No BHBF)

WY1998, [+,+] MLFF+HMF No Exotic Control [0,0] [+,-](No BHBF)

WY1997, [0,+] MLFF only No Exotic Control [0,0] [+,-](No BHBF)

WY1996, [0,+] Interim+BHBF No Exotic Control [0,0] [-,-](W/ BHBF)

WY1995, [-,+] Interim only No Exotic Control [0,0] [0,0](No BHBF)

WY1994, [-,+] Interim only No Exotic Control [-,-] [-,-](No BHBF)

WY1993, [-,+] Interim only No Exotic Control [0,-] [+,+](No BHBF)

WY1992, [-,+] Interim only No Exotic Control [-,-] [+,-](No BHBF)

WY1991, [0,0] EXP Flows No Exotic Control [0,nd] [-,-](No BHBF)

Beach/Habitat

Building Flow

(Paria, LCR River 

Sand Inputs

Relative to Historic

Mean)

[+, 0, -]

Naturally Varied 

Temperature

(Relative to August Average 

at GCD, RM61)

[+, 0, -]

Mechanical

Removal of Rainbow Trout in

GC

(with Progressive

Optimization)

Dominant Dam

Operation

(with Seasonal Variants

Toward “Designer 

Flows,” but All Within

ROD)

Water Year, w/

HBC & RBT

Recruitment

Success

[+ or -]

Figure 3.3. A Historical Portrayal of the MLFF operation, as well as selected indicators 

for Rainbow Trout and Humpback Chub recruitment success (shown in terms of [+, 0, or 

-] data from AG&F, plus GCMRC and earlier data) shown in brackets within column #1 

next to Water Year, plus historical implementation of coldwater exotic fish control 

(column #2), history of sand production relative to the long term mean data for the Paria 

and Little Colorado Rivers [+, 0, or -] and the occurrence of BHBF tests since the end of 

the “No Action” era. This history portrays the evolution toward a Forward Titration 

through time, with addition of Mechanical Removal and natural warmer releases about 

equivalent to what would occur with the proposed Selective Withdrawal Structure. A 

major decision point occurs in WY 2006 with respect to construction of a Selective 

Withdrawal Structure at GCD. 

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Figure 3.4 Potential Factorial Design with Decadal Scale Time Blocks 

SWS Could Allow Factorial Design w/ Decade Scale Blocks

IMPLEMENT TREATMENT TREATMENT NOT IMPLEMENTED

WY2013, [?,?] Amended MLFF? Perhaps Stop EXP MR? Action [++,++] ???

WY2012, [?,?] Amended MLFF? Experimental Fish Removal Management [++,++] ???

Experimental Fish Removal Through [++,++] ??? *WY2011, decision MLFF ? Added)

[?,?]

WY2010, [?,?] MLFF only Might be Experimental Fish Removal Extended [++,++] ???

WY2009, [?,?] MLFF only Sand Bars Experimental Fish Removal Regime [++,++] ???

WY2008, [?,?] MLFF only Tests for Experimental Fish Removal Warm Thermal [++,++] ???

WY2007, [?,?] MLFF only (Ramping Experimental Fish Removal SWS Built? [++,++] ???

??? (No BHBF) MLFF Experimental Fish Removal [++,++] +Fall Testing *WY2006, decision

[?,?]

[+,+] (W/ BHBF) MLFF+EXP FF+Fall Experimental Fish Removal [++,++] Testing

WY2005, [?,?]

WY2004, [?,0] MLFF+EXP FF Experimental Fish Removal [+,+] [-,-] (No BHBF)

WY2003, [?,-] MLFF+EXP FF Experimental Fish Removal [+,+] [-,-] (No BHBF)

WY2002, [?,-] MLFF only No Exotic Control [0,0] [-,-] (No BHBF)

WY2001, [?,+] MLFF only No Exotic Control [0,0] [+,-] ( No BHBF)

WY2000, [+,+] MLFF+LSSF+HMF No Exotic Control [0,+] [-,-] (No BHBF)

WY1999, [+,+] MLFF only No Exotic Control [0,0] [+,- ] No BHBF)

WY1998, [+,+] MLFF+HMF No Exotic Control [0,0] [+,-] (No BHBF)

Beach/Habitat

Building Flow

(Paria, LCR River

Sand Inputs 

Relative to Historic

Mean)

[+, 0, -]

Naturally Varied 

Temperature

(Relative to August Average

at GCD, RM61)

[+, 0, -]

Mechanical

Removal of Rainbow Trout in

GC

(with Progressive

Optimization)

Dominant Dam

Operation

(with Seasonal Variants

Toward “Designer 

Flows,” but All Within

ROD)

Water Year, w/

HBC & RBT

Recruitment

Success

[+ or -]

Figure 3.4. Conceptual Phase V Experimental Design Depicting How Addition 

of a Selective Withdrawal Structure Might Be Used to Continue A Warm 

Release “block” Along with Ongoing Mechanical Removal of Warm and 

Coldwater Exotic Fishes Below Lees Ferry, Along With Occasional Sediment 

Triggered BHBF’s. If a strong HBC recruitment signal is detected between 2004 

and 2011, then this Forward Titration design can be evolved into a full Factorial 

experimental design, if, either Mechanical Removal or Thermal treatments or 

discontinued at the end of Phase V. Continuation of the MLFF operation is the 

only policy so far that has been approved as a “management action.” In the 

event that a strong HBC recruitment signal is not detected between 2004 and 

2011, a decision could be made to continue managed warming and exotic fish 

control, along with implementation of stable flows throughout some portion of 

the year for several years as a continuation of the Forward Titration. 

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G. FY 2007-2011 Short Term Research Studies to Address Knowledge Gaps 

Research that is designed to address questions that are identified through the 

knowledge assessment process include single projects as well as complex 

programs of research that involve multiple projects within a program. An 

example of the latter is the aquatic food base program initiative that includes 

 Stable isotope research 

 Instream metabolism quantification 

 Secondary production, etc. 

Individual research projects addressing critical knowledge gaps include native 

fish translocation, population genetics of HBC, Early life history of Rainbow 

trout in Lees Ferry, aeolian deposition and archaeology site preservation. These 

projects and programs as well as others are presented in Chapter 4 discussions of 

research. 

 

H. FY 2007-2011 Research Studies to Develop New Monitoring Procedures 

Research to improve monitoring methods is a critical component in the adaptive 

management program. Providing meaningful monitoring results to managers 

about resources is a basis for deciding if and how operations may be improving a 

targeted resource. The resources that are targeted for monitoring methodology 

review and research are in the areas of aquatic biology and cultural resources. 

They include: 

 

• Predatory fish assessments – improving detection and capture 

methods for warm and cold water exotic species 

• Water quality – downstream and reservoir modeling to evaluate 

sampling frequency and parameters. 

• Relationship of riparian vegetation to drift – determining the 

contribution and importance of riparian vegetation to trophic food 

webs and determining effective approaches to quantify vegetation. 

• Archaeological site monitoring indicators – identification and 

refinement of methods and variables that will be used to assess 

erosion of archaeological site relative to dam operations and visitor 

impacts. 

CHAPTER 4. LINKING MONITORING AND RESEARCH PROJECTS TO 

MANAGEMENT GOALS AND INFORMATION NEEDS 

Various reviews of the GCFS and GCMRC science programs have been conducted in 

the 1980s, 1990s and 2010s by NRC, PEP panels and Science Advisors. A concern over 

this period has existed that more comprehensive ecosystem science approaches are not 

being utilized. The new proposed science planning direction of GCMRC will 

incorporate the ecosystem science paradigm as presented by various program constraints 

including budget, logistics, technology, etc. 

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The new proposed science program incorporates efforts in experimentation with flow 

and non-flow management alternatives, research to develop needed information for 

managers and research to develop new monitoring procedures. The monitoring program

is reoriented toward core monitoring information needs. 

The strong concerns of managers regarding status of selected CRE resources including 

HC and recreation beaches has resulted in GCMRC and the GCD-AMP pursuing a 

hybrid science design that attempts to obtain positive effects in selected resources while 

obtaining as much knowledge as possible. 

The experimentation program will evaluate, as an example, over the 2007-2011 period, 

the effects of high flows, warm water, predation control, and stable flows on humpback 

chub lifecycles, sand bars, food web, etc. 

Critical research studies will support experimentation, and will evaluate example, CRE 

food base, humpback chub translocation within the Little Colorado River, modeling sand 

dynamics and loss, etc. Extensive research studies will be focused on improving 

knowledge related to enhanced survival and recruitment of any back chub, including 

aspects of predation, food base, genetics, refugia, etc. A similar intense effort will be 

pursued in modeling of sand loss to the system, and contributions riparian vegetation to 

the system. 

Research studies will also be used, for example, to design new monitoring protocols for 

food base, control of warm and coldwater exotic fishes and assessment of gear types and 

efficiencies for monitoring warm water fishes, changes in pathogens in the CRE, etc. 

The monitoring program elements presented in this chapter are redesigned to address the 

core monitoring information needs of managers and stakeholders and will emphasize 

native fish populations, water quality, cultural resources, etc. 

Strategies will be pursued so that developed research and monitoring data more closely 

track changes in critical resources at levels of resolution required in the advisory process 

associated with the GCD-AMP. 

Following, are examples of research program efforts addressing managers’ information 

needs through the ecosystem science format: 

A. Social Resources Goal: Providing Power Generation. 

1. Issues of Concern: 

Maintaining programmed power operations; obtaining replacement 

power; exceeding operating criteria. 

2. AMWG Goal #10. “Maintain power production capacity and energy 

generation, and increase where feasible and available, within the 

framework of the adaptive management competing goals.” 

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3. There are extensive ecosystem implications of flow changes to increase or

decrease power. Flow levels, ramp up and ramp down rates, flow temporal 

variation etc. can effect physical, biotic and socio-cultural resources 

positively or negatively. Knowledge assessment of power generation in 

this system indicates that wide variations in high/low daily flows and 

hourly ramping rates are beneficial to power, but potentially not beneficial 

to other resources. The economic trade-offs to make informed decisions 

are knowable owing to abundant data and protocols to track resource, but 

these data are not well documented nor accessible to all stakeholders. 

 4. Overarching science question: 

a. What flow regimes best mitigate cultural, sediment and recreation 

resource impacts, improve fishery resources, maintain or improve 

riparian habitat and insure acceptable power generation? 

5. Proposed science program for study of power operations: 

a. Research programs 

Develop simulation sub-model to produce variable power and water 

opportunity costs for alternative flow regimes.

b. Monitoring Program 

Monitor water and power variability and associated changes in other 

resources. [Include looking outward matrix diagram here (see next 

section for example of this)] 

B. Physical Resource Goal: Downstream water temperature including 

implications of utilizing a Selective Withdrawal Structure (SWS). 

1. Issues of Concern. Current natural warming of the CRE (2004-2007?) offers 

potential for evaluating some aspects of a TCD. Warm water temperature 

could have positive effects (e.g., HBC recruitment), but also negative effects, 

(e.g., higher HBC predation). The net effect becomes the critical issue and 

therefore the risk associated with TCD implementation must be fully 

evaluated through use of sub model simulations. An operational grade 

downstream water temperature sub-model would be valuable for other 

resource assessments as well and development of such a model is embraced 

within the context of the “looking outward” matrix approach (Figure 4.1). 

Model development has been initiated and can be quickly developed to the 

needed level with some additional work. 

2. AMWG Goal #7. “Establish water temperature, quality, and flow dynamics 

to achieve the adaptive management program ecosystem goals.” 

3. Ecosystem implication of variable water temperatures are most paramount 

regarding biotic resources i.e., potential enhanced HBC habitat, movement of 

21
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warm water predators up river. However, social resource impacts could be 

significant, if for example, HBC are negatively impacted by warm water 

predators, or pathogens increase and impact RBT numbers or condition. The 

looking outward matrix demonstrates temperature (see attached figure) to be 

influenced primarily by flow and power resource objectives. Knowledge 

assessment recently identified that changing temperature has significant 

impact on almost all biology in the CRE and can also influence suspendedsediment transport rates and recreational experience. Some knowledge exists 

regarding longitudinal main channel water temperature changes, however 

increased knowledge is needed about the influence of tributary, LCR, and 

Lake Powell elevation and regional climate influences. A multi-dimensional 

sub-model for downstream temperature has already been developed by Bruce 

(GGEMS), but needs to be more fully evaluated, verified and incorporated 

into the ecosystem science program (made accessible to other scientists and 

fully linked to other sub-models, such as the CE-QUAL2 model for Lake 

Powell). 

4. Two significant overarching questions relating to this resource goal are: 

a. How do dam operations, reservoir conditions, tributaries, climate, canyon 

orientation/aspect, and the proposed temperature control device affect water 

temperature along the Colorado River in Grand Canyon, both in the main 

channel (1-dimensional) and in near-shore habitats (2 & 3-dimensional 

elements that tie 1-D responses to temperatures within backwaters)? 

b. How does water temperature affect other water quality parameters and 

other resources such as the aquatic food base, fish, biological pathogens, 

recreation, etc? Question b. is determined via actual monitoring and 

research of other resources such as RBT, HBC, food base etc. However 

Question a. can be pursued under water quality, through several other subquestions of a., including; 

• What would release temperatures and downstream near-shore 

temperature be like under prolonged drought conditions? 

• How do backwater temperatures in the vicinity of the LCR differ 

under differing fluctuating versus steady flow alternative? 

• What temperature would the main channel achieve at a given 

location during a low steady flow during a typical summer with a 

TCD in place? 

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Actions 

Figure 4.1. The Outward Looking Matrix for the Mainstem Temperature Sub-Model. 

5. Proposed science program:

 a. Research Program

• Collaborate with BOR engineers to refine, improve 

development of water temperature predictive model 

• Evaluate and verify model performance and link with other 

sub-models through advanced conceptual modeling efforts 

• Synthesis of Lake Powell for the purpose of modeling and 

monitoring program assessment 

• Synthesis of historic tributary data (e.g., LCR) 

• Temperature Control Device 

• Constrained fluctuations to stable flows 

• On-going reservoir depletions 

• Surplus criteria ROD 

• Conjunctive Use agreement 

Mainstream Temperature 

Sub-Model

Indicators 

• Recruitment of Native Fish 

(HBC). 

• Mainstem spawning and 

recruitment of native fish. 

• Lees Ferry RBT abundance 

• Primary and secondary

production 

• Safer and improved 

recreational experience 

Output from other submodels and 

data sets 

• QW 

• Suspended sediment 

monitoring 

• Other QW 

monitoring/modeling

(nutrients, CEQUAL2) Input to other submodels and data sets • Meterological monitoring 

• Food base productivity

monitoring • QW monitoring 

o Mainstem temp model 

GEMS (2&3-D 

nearshore) 

• Fisheries Monitoring 

• Stock assessment (native 

fish, non-natives, LF 

trout) • Meterological data 

• Reservoir / climate analysis • Disease/parasite

monitoring • Tributary synthesis 

• Recreational evaluations • Recreation 

• Rafting/angling 

evaluation 

• Creel Survey

• Public Health 

• Power evaluations

• Cultural valuations 

• Lake Powel model 

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b. Monitoring Program

• Model calibration and verification, tracking changing 

boundary conditions (CE-QUAL2; GSTARS, UNSTEADY; 

GGEMS). 

• Anticipate QW w/nutrients in support of aquatic resources 

(e.g., food base monitoring). 

• Surface water and temperature measurements at discrete 

points (e.g., tributary inputs to Lake Powell, forebay, GCD 

penstocks, Lees Ferry, LCR, Grand Canyon and Diamond 

Creek, plus major downstream tributary inputs). 

 

C. Physical Resource Goal: Restoring Sand Bars and Maintaining Related 

Habitats. 

1. Issues of Concern: 

Feasibility under the Record-of-Decision of restoring and maintaining 

sand bars at levels needed to achieve priority ecosystem objectives. 

2. AMWG Goal #8: “Maintain or attain levels of sediment storage within 

the main channel and along shorelines to achieve the Adaptive 

Management Program ecosystem goals.” 

3. Ecosystem implications of restoring and maintaining physical sand bar 

habitats and main channel sediment storage below Glen Canyon Dam can 

affect other physical, biotic and socio-cultural resources. Impacts to 

socio-cultural and biotic resources from releasing controlled floods during 

seasons of sediment input (summer and fall) relative to originally 

proposed spring timeframe (DOI, 1995). Additional socio-cultural and 

biotic resource impacts from constraining releases (summer through fall 

or winter to spring) so as to retain or bank fine sediment tributary inputs 

until spring timing for floods. This strategy might gain increased 

turbidity, and influence of finer grained sediments in shoreline stored 

bars, but adversely influence primary productivity. Knowledge 

assessment identified flow regimes required to bank tributary-input sand 

supplies (~10,000 cfs or lower) and identified that fine-sediment 

enrichment is required to achieve sandbar restoration. Even under supply 

enrichment, sand bars can only be significantly restored by elevating 

flows above power plant capacity, but the required high-stage flow 

depatures may only be needed for short periods. For new sand bars to 

persist, the deposits need to be substantially isolated from the erosional 

influence of daily fluctuations. The basis for on-going sediment 

conservation research is that the EIS paradigm has been falsified. This 

leads to one overarching question regarding sediment sustainability. 

24
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4. Overarching Science Question: Is there a “flow-only” (meaning, without 

sediment augmentation) operating strategy for Glen Canyon Dam releases 

that will attain and maintain necessary levels of useable sediment storage 

in the Colorado River ecosystem (CRE) to achieve desired CRE resource 

conditions and ecosystem function? Assumption: artificial floods, 

termed Beach/Habitat-Building Flows, are a required element of the flowonly management strategy. [Include sand mass-balance diagram here 

comparing EIS rating curve prediction versus measurement data] 

5. Proposed science program for determining whether or not a flow-only 

strategy for maintaining sediment will be possible. 

a. Research Program

• Tied to large scale experimentation (potential replication of the 

2004 sediment test, but perhaps in alternate season of spring) 

• Ongoing flow and sediment-transport model development and 

refinement (both for major tributaries and main channel 1-

dimensional sand routing to predict fate of inputs under varied 

supply conditions and operations) 

 b. Monitoring Program

• Relative to concept of sustainability of sand bars and related 

experiments, develop event monitoring in support of 

experimental research and modeling associated with both 

tributary sand production and mainstem suspended flux. 

• Focused monitoring around required parameters associated with 

boundary conditions required as input by sediment sub-models. 

• Sand bar and eddy storage data collected around controlled 

flood events that are required to verify the sediment submodels. 

• Stage measurements at key locations that are needed to verify 

flow routing sub-models. 

D. Biological Resource Goal: Protection of CRE Food Base 

1. Issue of Concern: 

Determining what is the contribution of primary and secondary productivity 

and critical pathways in the aquatic food web, and how operations 

(temperature, monthly volumes, daily range) affect productivity and food 

web dynamics. 

2. AMWG Goal #1: “Protect or improve the aquatic food base so that it will 

support viable populations of desired species at higher trophic levels.” 

3. Ecosystem implications of significant changes in aquatic food base can affect 

higher tropic levels such as RBT and HBC. Looking outward matrix 

25
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assessments of knowledge of effectors upon and impacts to this resource in 

the CRE are incomplete (Figure 4.2). A knowledge assessment determined 

that the flux of invertebrates is expected to increase with temperature, but that 

the directional response in Grand Canyon is unknown. Higher temperatures 

and increased primary production would likely lead to increased invertebrate 

production and drifting rates. In Grand Canyon, relative availability of in

stream production vs. terrestrial inputs is unknown. Although increased 

temperatures lead to increase algae production, the amount of terrestrial 

inputs will not increase. Thus, in Grand Canyon, basal production numbers 

will not increase, and it is unknown whether invertebrate production and drift 

rates will increase with temperature (see section B., part 4b). Dam operations 

(e.g., daily range, monthly volumes) also differentially affect productivity and 

drift. 

4. Overarching science questions exist in at least three areas as follows: 

 

a. Basic understanding of food web linkages: What are the important 

pathways, and the rate of flux along them, that link lower trophic levels 

with fish? 

b. Relational understanding of productivity and operational affects: How 

is invertebrate flux affected by water quality and dam operations?

c. Linkage between food availability (local and drifting food) and fish 

abundances. Are trends in the abundance of fish populations or indicators 

associated with fish, correlated with patterns in food availability and/or 

quality? 

5. Proposed science program for the aquatic food base: The science program 

includes research to address questions in area 4a. and c. that takes a multipart approach to identify critical pathways in the aquatic food web. The 

monitoring program will be developed based on research results and will be 

able to address 4b. through changes in operations. 

 a. Research program

• Whole river metabolism 

• Stable isotope/diet analysis 

• Carbon/energy transfer from basal level through invertebrates 

(secondary production) 

• Bioenergetics modeling 

b. Monitoring program – TBD but may include a combination of

• Bioenergetics modeling 

• Whole river metabolism 

• Secondary producer monitoring 

• Fish diet sampling 

• Fish abundance data from fisheries program

26
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Actions 

Figure 4.2 The Outward Looking Matrix for the Aquatic Food Web Sub-Model. 

E. Biological Resources Goal: Maintain Lees Ferry Rainbow Trout Fishery

1. Issues of Concern: 

Potential impacts of Lees Ferry rainbow trout program on downstream

native fishes. Inability to sustain quality RBT in a naturally reproducing 

fishery. 

2. AMWG Goal #4: “Maintain a naturally reproducing population of 

rainbow trout above the Paria River, to the extent practical and consistent 

with the maintenance of viable populations of native fish.” 

3. Ecosystem implications of maintaining a naturally reproducing 

population of rainbow trout above the Paria River. The goal of upstream

population abundance (100,000 adults) may cause downstream migration 

and increased downstream competition and predation on native fishes by 

• Temperature Control Device 

• ROD flows 

• Stabilized flows

• On-going reservoir depletions 

• Surplus criteria ROD 

• Conjunctive use agreement 

• Mechanical removal 

Aquatic Food Web 

Sub-Model

Indicators

• Drift rates 

• Primary and secondary

production 

• Fish diet 

• Fish condition factor 

• Fish abundances 

Output from other sub-models and 

data sets 

• QW 

• Suspended sediment 

monitoring 

• Other QW 

monitoring/modeling

(nutrients) 

Input to other sub-models and data 

sets 

• Meterological monitoring • QW monitoring 

• Fisheries Monitoring o Mainstem temp model 

• Stock assessment (native • Meterological data 

fish, non-natives, LF 

trout) 

• Reservoir / climate analysis

• Bioenergetic model 

• Disease/parasite

monitoring 

• Tributary synthesis 

• Recreational evaluations

• Recreation 

• Angling evaluation 

• Creel Survey

• Public Health 

• Power evaluations

• Lake Powel model 

27
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migrant rainbow trout. Recreational fishing interactions could increase 

pathogen prominence. A knowledge assessment recognized that the 

relationship between Lees Ferry and downstream RBT populations needs 

to be determined. Monthly volume changes can affect survivorship of 

young fish in Glen Canyon. Growth rates in YOY are affected by 

stability of flows and temperature. 

4. Overarching Science Questions: 

a. Operational affects on recruitment dynamics and dispersal. What

is the relationship between GCD flow regimes, and annual volumes, 

and population dynamics of rainbow trout in the Lees Ferry reach 

and downstream?

b. Operational affects on recruitment dynamics in Lees Ferry. What

could be the water quality effects (temperature) on RBT/Brown trout 

in Lees Ferry? 

5. Proposed science program for study Lees Ferry rainbow trout: 

a. Research programs and strategies 

• Research plan to evaluate Lees Ferry migration downstream. 

• A research study to evaluate temperature regimes on RBT 

 b. Monitoring Program 

• Monitor changes in trout condition under differing temperature 

regimes. 

• Stock assessment for Lees Ferry linked with downstream RBT 

monitoring. 

• Monitoring of brown trout occurrence in L.F. 

F. Biological Ecosystem Resource Goal: Maintain or Enhance Native Fish 

Populations [photos of native fishes here] 

1. Issues of concern. 

Two factors likely responsible for the decline of native Colorado River 

fishes are physical-habitat modification (water quality parameters, such 

as thermal regime or others within main channel and tributaries, as well 

as shoreline habitat stability), and interaction with non-native species. 

However, there are fundamental uncertainties regarding how these 

factors, and perhaps others, influence native fishes. It has been shown 

that the decline of native fishes in some parts of the Colorado River basin 

is a result of continued recruitment failure and is suspected for humpback

chub in Grand Canyon. Questions remain about how impacts at various 

life stages may control overall humpback chub population dynamics. It is 

not clear which factors (e.g., habitat modification, non-native species 

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interactions, or other factors) are dominant drivers of humpback chub 

population dynamics. 

2. AMWG Goal #2: “Maintain or attain viable populations of existing 

native fish.”

3. Ecosystem implications relative to maintaining native fish components 

are broad due to inter- and intraspecific interactions of fishes, trophic 

level linkages that involve water quality, food availability and quality, 

and the interactions each of these resource has with flow and 

temperature. The looking outward matrix identifies extensive effectors 

on HBC and illustrates the complex interactions that HBC have with 

other resources as flows change. The knowledge assessment identified 

the uncertainty around improved growth with warm temperatures 

balanced against food availability as fish metabolism increased. Habitat 

stability relative to early life history survivorship of native fish has scant 

data to support enhanced growth rates, though some data exist for 

interactions of growth and stable habitats for YOY rainbow trout in Glen 

Canyon. 

4. Overarching science questions. Two overarching questions must be 

resolved regarding HBC. 

a. Environmental affects on recruitment dynamics. What is the 

limiting life stage controlling recruitment of the HBC? 

b. Environmental affects on recruitment dynamics. What are the 

dominant factors controlling recruitment of HBC?

5. Proposed science program for the native fish program involves extensive 

research and monitoring: 

 a. Research program

• Improving monitoring technologies (gear efficiency and 

detection) and data analysis – field/lab based 

• Assessment of mortality factors (habitat, predation, 

competition) for life history parameters – lab and controlled 

field experiment 

• Monitoring protocol development for disease and parasites. 

• Exotic control efficacy 

• Efficacy of developing sampling protocol/approach for 

estimating YOY survivorship. 

• Evaluate relative importance of temperature, fluctuations and 

food quality/availability on survival and growth of YOY 

native fish. – modeling and controlled field experiment 

29
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 b. Monitoring program

• Stock assessment of LCR HBC, Flannelmouth sucker, as 

possible. 

• Abundance and distribution of mainstem fishes. 

• Stock assessment of non-natives, as possible. 

• Lees Ferry Rainbow Trout monitoring. 

G. Biological Ecosystem Resource Goal. Maintain or improve riparian and 

spring communities including endangered species [photo of Vaseys Paradise 

and kanab ambersnail here] 

1. Issues of Concern. 

Riparian plant communities are linked to both aquatic and terrestrial 

resources (secondary production, cover), and interacts with cultural 

resources associated with recreation (camping sites) and indirectly with 

archaeological sites. Understanding how riparian vegetation responds to 

flows and affects other resources of concern forms a basis for managing 

critical resources like native fish, archaeological properties and 

recreational components. 

2. AMWG Goals #5 & 6: “Maintain or attain viable populations of kanab 

ambersnail. Protect or improve the biotic riparian and spring 

communities including threatened and endangered species and their 

critical habitat.” 

3. Ecosystem implications of maintaining or improving riparian 

communities relate to aquatic and terrestrial food webs associated with 

native and sport fishes and riparian breeding birds including 

southwestern willow flycatcher, as well as other terrestrial wildlife. The 

looking outward matrix identifies flow and sediment inputs as primary 

effectors for riparian vegetation, but there are multiple sub-models to 

which the riparian community information is a contributor. The 

knowledge assessment recognized that there was some certainty about 

the relationship of marsh community development and flows, but that 

this certainty decreased as one progresses upslope. The interactions 

between wildlife and riparian habitat are less developed. 

 

4. Overarching science questions are as follows: 

a. Temporal and spatial interactions within the riparian 

community. How do processes occurring at a variety of spatial 

scales (i.e., population level to community to landscape scales) 

interface to influence riparian habitat structure and composition? 

b. Temporal and spatial interactions between ecosystem 

components. What is the nature and timing of terrestrial—aquatic 

linkages, and what is their influence on the recipient habitat? 

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c. Temporal and spatial interactions between ecosystem 

components. How do terrestrial habitat and cultural resources 

interface? 

5. Proposed science program for the riparian vegetation and springs 

communities involves synthetic research and monitoring: 

 a. Research program

• Vegetation synthesis 

o Quantify rates of change and assess sources of change 

o Utilizes physical science synthesis data 

o Incorporates scanning project for retrospective analysis of 

vegetation change. 

• Estimate above ground productivity and determine contribution 

to energy/carbon cycles – vegetation map – field sampling - 

modeling 

• Quantify vegetation encroachment in tandem with camp site 

assessments/inventory 

• Investigate the utility of remote survey of Vaseys Paradise

• Population modeling of KAS 

b. Monitoring program

• Annual system-wide measure of vegetation change related to 

annual operations. 

• Five – year overflight vegetation map to quantify community 

change. 

• Secondary production monitoring. 

• Riparian bird surveys/inventory – frequency to be determined. 

H. Sociocultural Ecosystem Resource Goal: Maintain high quality 

recreation experience in the CRE. 

1. Issues of Concern. 

Flows are known to be important influences of recreational experience. 

Importance of flows relative to other physical and social attributes that 

define a high quality recreational experience is less certain. Flows can 

affect recreational experiences in multidimensional respects. Evaluation 

of how flows affect recreation experience requires a trade-off analysis 

that considers not only the multiple and sometimes contradictory effects 

of flows on recreational experience, but also the effects of non-flow 

attributes (e.g., NPS management decisions about appropriate use levels, 

AZGF fishing regulation, etc.). Evaluations of recreation experience are 

coupled with NPS management goals for river-based recreation (e.g., 

maintaining wilderness qualities, access, and ecosystem function) and 

AZGF sport fishing management goals. Existing model (Roberts and 

others 2002) may be useful for evaluating how different flows interact 

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with other variables such as numbers of trips on the water, to shape the 

quality of recreational experiences. 

2. AMWG Goal #9: “Maintain or improve the quality of recreation 

experiences for users of the CRE, within the framework of the adaptive 

management program ecosystem goals.” 

3. Ecosystem implications of maintaining recreation quality are not fully 

understood, but recreational activities can potentially affect rates of 

sediment erosion, terrestrial and aquatic ecosystems functions (food base, 

water quality, animal behavior, etc.). Visitor use also impacts cultural 

resource integrity and wilderness qualities, both of which NPS is 

mandated to preserve. The looking-outward matrix identifies flow as a 

primary affector of key recreational experience attributes (e.g., campsite 

size, distribution, and qualities; angling success; rafting enjoyment; 

crowding; human health & safety.). Knowledge assessment identified 

the need to understand the importance of flows relative to other factors 

that may affect recreational experience. Subsequent knowledge gaps 

involved how the variables of flow interacted with other aspects of 

recreation along the river corridor (e.g., rafting vs. angling vs. camp site 

availability and flow) 

4. Overarching science questions are as follows: 

a. What are the principle drivers of recreational experience quality in the 

 CRE, and how important are flows relative to the other drivers?

b. How do dam-controlled flows and other management actions affect 

 recreational experiences, and what is/are the optional flows for 

 maintaining a high quality recreational experience in the CRE? 

5. Proposed science program for study of recreation-related issues 

 a. Research programs: 

• Establish importance of flow parameters relative to other experiential 

attributes in determining quality of recreational experience in the 

CRE. 

• Inventory current campsites; evaluate change in campsite 

size/distribution/qualities through time (1976-2006) using Weeden 

1976 inventory as baseline. 

• Apply NAU visitor encounter model (Roberts and others 2002) to 

predict crowding/congestion under varying proposed flow regimes. 

• Quantify recreational impacts from an ecosystem perspective (e.g., 

contributions to food base, human-induced sediment loss at beaches, 

vegetation impacts) focused on debris-fan complexes. 

• Define indicators of recreational experience, including human health 

and safety under varying flow regimes for future monitoring 

• Conduct trade-off analysis of key experiential attributes under 

varying flow regimes. 

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Actions 

Figure 4.3. The looking outward matrix for the recreation submodel.

b. Monitoring Program

• Monitor physical and social indicators of high quality visitor 

experiences (e.g., campable area, campsite 

competition/crowding.) 

• Monitor visitor impacts affecting ecosystem processes 

• Monitor human health and safety-related parameters under 

varying flow regimes 

• Dam Operations/Experimental flows 

• NPS use levels/access regulations

• NPS transportation regulations 

• AZGF fishing regulations 

Recreation Experience

Sub-Model

Indicators 

• Condition and abundance of 

LF Trout. 

• Recreational safety

incidences

• Campsite 

crowding/competition 

• Campsite area/qualities 

• Ecosystem resource

impacts from human uses 

Output from other submodels and • Visitor satisfaction 

data sets 

• QW 

• Suspended sediment 

monitoring 

• Glen Canyon releases

• Fisheries Monitoring 

• Stock assessment (nonnative fishes, LF trout) Input to other submodels and data sets 

• Disease/parasite

monitoring • Conceptual model of

ecosystem relationships 

under varying flows • Recreation 

• Rafting/angling 

evaluation • Vegetation dynamics 

• Cultural resource 

condition model • Creel Survey

• Public Health 

• River Trip Simulator 

• Power evaluations

• Cultural valuations 

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I. Socio-cultural Ecosystem Resource Goal: Ensure preservation of cultural 

resources. 

1. Issues of Concern. 

1) Maintaining physical integrity of cultural resource sites; 2) balancing 

diverse stakeholder values in relation to cultural resources (i.e., balancing 

the scientific information valued by scientists and the public, the 

educational/interpretive qualities valued by visitors, the 

traditional/religious values of tribes); 3) developing/evaluating 

appropriate mitigation strategies to offset resource loss. NPS 

management preferences (e.g., desire to preserve archeological sites in 

situ) limit options for future science and constrains possible management

directions. 

2. AMWG Goal #11: “Preserve, protect, manage and treat cultural 

resources for the inspiration and benefit of past, present and future 

generations.” 

3. Ecosystem implications of protecting and preserving cultural resources 

are not fully understood, but ongoing loss of Holocene deposits results in 

degradation of archaeological sites and also diminishes our ability to 

reconstruct/understand past ecosystem processes or interpret cultural 

resources in their prehistoric and historic contexts. Flows also affect the 

culturally-valued native plants in the CRE. Proposed experimental flows 

and non-flow treatments for archaeological sites can potentially affect 

recreation and tribally-valued traditions, as well as ecosystem processes 

(rates of sediment erosion, vegetation cover, etc.). The looking outward 

matrix (Figure 4.4) identifies flow regimes as one of several key factors 

affecting cultural resource conditions in the CRE. Knowledge 

assessment workshop identified need for well-conceived geomorphic 

model to assess relationship between flows, sediment transport, climatic 

factors and archaeological site erosion and for research to inventory, 

evaluate, and determine effects of flows and treatment activities to TCPs. 

4. Overarching science questions are as follows: 

a. How do flows, climate, and human use interact to impact historic 

properties in the CRE, and more specifically, do flows affect (increase or 

decrease) rates of erosion of the higher Holocene deposits where most 

archaeological sites occur? 

 Subquestions (of Question a):To what extent do flows affect 

archaeological site stability/integrity in the CRE? 

 If dam controlled flows are contributing to (influencing rates of) 

archaeological site/TCP degradation, what are the optimal flows 

for minimizing future impacts to these historic properties? 

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 To what extent and in what respects can BHBFs be used to 

achieve systemwide mitigation of archaeological site erosion? If 

flows or BHBFs can not be applied to benefit cultural resources, 

can other sustainable treatment options be applied for preserving 

threatened heritage resources in the Colorado River corridor, and 

what are the best (most effective and least intrusive) options for in 

situ preservation of cultural resources? 

b. How do flows positively or negatively impact the culturally-valued 

flora and fauna in the CRE (especially the biological communities 

associated with TCPs)? 

c. What important historical/legacy information about the CRE 

ecosystem and past human use of the CRE are embedded within the 

higher elevation Holocene deposits and will be lost due to the ongoing 

erosion of these older pre-dam deposits? 

5. Proposed science program for study of cultural resources: 

 a. Research Programs 

• Develop geomorphic model to predict and quantify erosion rates at 

archaeological sites under varying flow regimes, taking into account 

effects of climate, human use, and geomorphic parameters. 

• Map and evaluate ecological/cultural information embedded within 

CRE Holocene deposits. 

• Identify and evaluate TCPs and the flow-related processes that may 

be affecting them. 

b. Monitoring Programs 

• Monitor and quantify rates of erosion of Holocene terraces and 

and track physical changes affecting integrity of archaeological 

sites and TCPs to build geomorphic model, verify model 

predictions, and track status and trends of cultural resource 

conditions. 

• Monitor changes to specific plants/vegetation communities valued 

by tribes as resources of traditional concern. 

• Monitor effectiveness of proposed cultural resource treatments 

(e.g., check dams, long-term effects of BHBFs, etc. 

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Actions 

Figure 4..4. The looking outward matrix for the cultural resources submodel. 

J. Data Management Goal: Ensure Adequacy of Existing and Future Data 

1. Issue of concern. Adequacy, accessibility and relevance of existing data (data 

needed for modeling ecosystem interactions as well as assessing status & trends 

of key resources) needs to be assessed periodically to ensure that the AMP has 

the data it needs to fulfill its stated goals/objectives and maintain scientific 

credibility. 

2. AMWG Goal 12: “Maintain a high quality monitoring, research and adaptive 

management program.” 

• Dam Operations/Experimental flows 

• NPS use levels/access regulations

• NPS wilderness management goals 

• NPS cultural site preservation & data

recovery (treatment) activities

Cultural Site Erosion & 

Condition Sub-Model

Indicators 

• Rates of arroyo incision 

• Rates of nick point 

migration 

• Site surface topographic 

change 

• Ecosystem resource

impacts from human uses 

(trails, soil compaction,

crytobiotic crust trampling, 

vegetation impacts) 

• Visitor satisfaction 

Output from other submodels and 

data sets 

• WQ 

• Glen Canyon releases

• Suspended sediment 

monitoring 

• Weather station data 

• Sand storage models Input to other submodels and data sets • Sand bar changes 

detection model • Conceptual model of

ecosystem relationships 

under varying flows 

• Recreation Experience

• Rec. Exp Attribute 

evaluations • Vegetation dynamics • Visitor use patterns • Aeolian transport model • Other cultural valuations • Recreation Experience

submodel 

• Sand storage and flux 

(from tributary inputs) 

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3. Ecosystem implications are indirect, but this issue is important for future 

monitoring and modeling of ecosystem functions. 

4. Overarching Question: What is the status of existing GCMRC/AMP data 

related to key resources and ecosystem processes (such as water volume/release 

pattern, water temp/ qualities, sediment volume/flux, vegetation/habitats, 

terrestrial food resources, etc) with respect to the following: 1) accuracy of 

existing data, 2) adequacy/precision necessary for modeling and status/trends 

assessments, and 3) current accessibility/utility of existing databases for analyses 

and future model development. 

5. Proposed science program: Evaluate defined data needs relative to existing 

databases. 

 CHAPTER 5. A GOAL TO INTEGRATE ALL GCD AMP SCIENCE FOR 

IMPROVED KNOWLEDGE AND EFFECTIVE DECISIONS 

A. Extensive research, monitoring and management actions are now occurring in 

the CRE by various management and science groups. Although most are within 

the GCD AMP/GCMRC programs, managed with GCD AMP protocols, some

are not. 

 

B. A proposed SPG approach regarding “all non GCD AMP directed science” is to: 

1. Request TWG fully document all agency and other science programs in the 

CRE by FY 2006/2007. 

2. Evaluate potential implications of these activities to GCD AMP goals and 

objectives by 2007. 

3. Recommend to AMWG in FY 2007 approaches for GCD AMP to benefit 

from these programs and/or resolve any potential conflicts to GCD AMP 

 goals. 

CHAPTER 6. IDENTIFICATION AND DEVELOPMENT OF RESOURCE 

NEEDS FOR SUPPORTING SCIENCE PROCESS 

A. Defining generalized 2-year and 5-year GCMRC budgets 

1. The GCMRC will organize administratively within its own staff and in 

collaborative partnerships with other groups to improve its science capability 

 to resolve GCD AMP resource issues. 

 

a. The Center’s policy, development and science leadership effectiveness in 

this planning period is predicated on its ability to design and implement, 

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with diverse cooperators and leading cooperative and contract scientists, 

several new resource development efforts and critical systems-based 

biology, sediment and cultural science efforts. This will include 

aggressive leadership from the GCMRC Chief in new collaborative 

partnerships and aggressive science leadership for increased 

understanding of HBC population enhancement, opportunities and 

procedures to understand and improve CRE aquatic food base 

capabilities and non-native fish predation and pathogen control 

mechanisms. This requires positions in systems and fish ecology at the 

Center and development of both cooperative and contractual programs 

external to GCMRC for resource support and to gain expertise in 

modeling, food base and native and non-native fish ecology. Some

cooperative science programs are in place such as RBT programs and 

non-native fish depredation programs. Others such as riparian vegetation 

contribution to drift, systems understanding of aquatic food base and 

predation and pathogen programs must be developed. A sediment 

program effort to understand fine sediment loss to the system will be 

pursued in both cooperative and contractual modeling programs, and new 

approaches to cultural resources monitoring, research and preservation 

will involve both cooperative and contract programs. 

b. The FY 2007/2008 budget will reflect the beginning efforts in this 

planning period to resolve key AMWG concerns. New collaborative 

partnerships will be forged by the GCMRC Chief to assure success of

these programs. Revisions in the budget may be necessary to increase 

aquatic food base knowledge, especially as it relates to HBC needs, 

including vegetation contributions to drift; critical HBC life cycle 

constraints; fine sediment maintenance in the mainstem; and new 

approaches for cultural resources protection. It is anticipated that the 

additional funds needed for these efforts can be obtained through 

GCMRC leadership. In 2007, GCMRC will propose opportunities for 

collaborative partnerships to expand external resource capability to the 

Center to support expanded AMWG information needs. 

 B. Specifying desired collaborative programs and partnerships. The GCMRC 

has had to respond to many new science and administrative issues in the past 5 

years; i.e., non-native fish removal, sandbar building, reductions in budget, etc. 

Looking forward over the next five year planning period it will be necessary to 

do improved budget planning with the AMWG, using new AMWG protocols. 

Support from AMWG is necessary in the area of priority setting on programs and 

assisting GCMRC with budget support and new collaborative programs. To 

respond to the expanding science needs in the CRE, GCMRC and AMWG must 

build additional program capability in several areas. 

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1. AMWG should implement a 3-5 year cycle of revisiting its priority setting 

exercise for AMWG goals and information needs, to assist GCMRC in 

 program reductions and program realignment under constrained budgets. 

2. AMWG should develop greater support from the Secretary/Congress to 

prevent budget cuts and expand budgets when AMWG feels programs 

 should be expanded. 

3. GCMRC will formally program an in depth knowledge assessment and 

significant program revisions at 5 year intervals to align future science 

activities with AMWG priority goals.

4. GCMRC, with AMWG assistance, will program expanded collaborative 

 partnerships to increase resource capability in three areas. 

a. Develop formal cooperative partnerships with GCD AMP agencies 

 on associated GCD AMP programs to reduce GCD AMP program

cost or effort; i.e., NPS, BOR, SWSC, USF&W, etc. 

b. Develop formal collaborative partnerships with federal and state 

 agencies not currently involved in GCD AMP, but interested in GCD 

AMP programs; i.e., other federal and state agencies. 

c. Develop formal collaborative partnerships with other organizations and 

 foundations with interest in GCD AMP programs, i.e., NRCS, NSF, 

Museums, and Foundations. Collaborative efforts will be extended to 

 organizations interested in formal information technology partnerships 

with GCMRC, a program that must remain continually at the cutting 

 edge. 

39