Missouri Headwaters 

Basin Study

Mission Statements

The U.S. Department of the Interior protects and manages the 

Nation's natural resources and cultural heritage; provides scientific and 

other information about those resources; and honors its trust 

responsibilities or special commitments to American Indians, Alaska 

Natives, and affiliated Island Communities.

The mission of the Bureau of Reclamation is to manage, develop, 

and protect water and related resources in an environmentally and 

economically sound manner in the interest of the American public.

Montana Department of Natural Resources and Conservation's 

mission is to help ensure that Montana's land and water resources 

provide benefits for present and future generations.

Technical Memorandum Number. ENV-2020-081
Missouri Headwaters Basin Study

i 

Acronyms 

°F degree Fahrenheit

AEES Advanced Engineering and Environmental Services 

ARM Administrative Rules of Montana 

Basin Study Missouri Headwaters Basin Study 

BHWC Big Hole Watershed Committee 

BLM Bureau of Land Management 

CCAA Candidate Conservation Agreements with Assurances 

CE Common Era 

cfs cubic feet per second

CT Central tendency climate scenario 

EOWY end of water year

ESA Endangered Species Act

FERC Federal Energy Regulatory Commission 

FSID Fort Shaw Irrigation District 

gcpd gallons per capita per day 

GID Greenfields Irrigation District

GPMU Great Plains Management Unit 

HD Hot-dry climate scenario 

HUC8 sub-basins Hydrologic Unit Code eight-digit level drainage areas 

HW Hot-wet climate scenario 

Impacts 

Assessment

Upper Missouri Basin Impacts Assessment

IWRP Integrated Water Resources Plan 

LD longest drought 

LP longest pluvial (wet period)

MBMG Montana Bureau of Mines and Geology 

MCA Montana Code Annotated

MID most intense drought 

MIP most intense pluvial 

M&I municipal and industrial 

Montana DFWP Montana Department of Fish, Wildlife and Parks

Montana DNRC Montana Department of Natural Resources and 

Conservation 

msl mean sea level
Acronyms

ii

MW megawatt

NDRP National Drought Resilience Partnership 

NEPA National Environmental Policy Act

NHPA National Historic Preservation Act 

NGO non-governmental organization

PSMBP Pick-Sloan Missouri Basin Program 

RCM Revised Codes of Montana 

Reclamation Bureau of Reclamation

SECURE Water 

Act

Science and Engineering to Comprehensively 

Understand and Responsibly Enhance (SECURE) 

Water Act (Public Law 111-11, Subtitle F of Title IX, 

§9501 – §9510) 

SNAPP Science for Nature and People Partnership

State Water Plan 2015 Montana State Water Plan

UMH Upper Missouri Headwaters 

UMOWA Upper Missouri Watershed Alliance 

USACE U.S. Army Corps of Engineers

USDA U.S. Department of Agriculture

USFWS United States Fish and Wildlife Service

USGS United States Geological Survey

VIC Variable Infiltration Capacity hydrologic model

WaterSMART Water Sustain and Manage America’s Resources for 

Tomorrow 

WCFC Willow Creek Feeder Canal

WD Warm-dry climate scenario 

WW Warm-wet climate scenario
Missouri Headwaters Basin Study

iii

Contents

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

1.1. Basin Study Purposes and Objectives ........................................................................................ 1

1.2. Location and Description of the Missouri Headwaters Study Area ............................... 4

1.3. Water Use and Development........................................................................................................ 6

1.3.1. Irrigation..........................................................................................................................................................6

1.3.2. Hydropower Facilities .............................................................................................................................12

1.3.3. Municipal and Domestic........................................................................................................................16

1.3.4. Environment ...............................................................................................................................................17

1.4. Groundwater Resources ................................................................................................................ 22

2. Characterization of Historical and Projected Future Conditions.............................23

2.1. Historical Challenges and Considerations .............................................................................. 23

2.1.1. Population Growth...................................................................................................................................25

2.1.2. Closed to Further Water Appropriations........................................................................................25

2.2. Future Challenges and Considerations .................................................................................... 27

3. Collaboration and Outreach .......................................................................................33

3.1. Background and Preliminary Outreach ................................................................................... 33

3.1.1. Upper Missouri Impacts Assessment Technical Meeting in Bozeman, Montana, 

July 9, 2015................................................................................................................................................. 33

3.1.2. Missouri Headwaters Impacts Assessment and Basin Study Workshop in 

Helena, Montana, December 1, 2016..............................................................................................34

3.1.3. Upper Missouri Headwaters (UMH) Basin Task Force Meeting in Bozeman, 

November 8, 2017...................................................................................................................................34

3.2. Local Meetings .................................................................................................................................. 35

3.3. NDRP Montana Pilot Project ....................................................................................................... 36

3.4. Meetings with Other Entities ....................................................................................................... 36

3.5. Professional Meetings and Presentations .............................................................................. 37

3.6. Learning and Collaboration Opportunities ............................................................................ 37

4. Interrelated Activities ................................................................................................. 39

4.1. Montana State Water Plan ........................................................................................................... 39

4.2. The Montana Climate Assessment ............................................................................................ 39

4.3. City of Bozeman Integrated Water Resources Plan ............................................................ 40

4.4. Drought Planning ............................................................................................................................. 40

4.4.1. National Drought Resilience Partnership.......................................................................................40

4.4.2. WaterSMART Drought Contingency Planning.............................................................................41

4.5. Water Compacts ............................................................................................................................... 41

4.5.1. Blackfeet Tribe Compact .......................................................................................................................41

4.5.2. Chippewa Cree Tribe-Montana Compact ......................................................................................42

4.5.3. Missouri Wild and Scenic River ..........................................................................................................42

4.5.4. Upper Missouri River Breaks National Monument.....................................................................43

4.5.5. United States National Park Service................................................................................................. 43

4.5.6. United States Fish and Wildlife Service...........................................................................................43

4.5.7. U.S. Forest Service....................................................................................................................................43

5. Scenarios and Analysis................................................................................................45

5.1. Water Supply Scenarios ................................................................................................................. 46

5.2. Water Demand Scenarios ............................................................................................................. 48

5.3. Upper Missouri RiverWare Planning Model .......................................................................... 49

5.4. Strategy Assessment Measures .................................................................................................. 50
Contents

iv

6. Strategies .....................................................................................................................53

6.1. Formulation of Strategies ............................................................................................................. 53

6.2. Objectives and Constraints........................................................................................................... 53

6.3. Approach to Strategy Identification ......................................................................................... 53

6.4. Approach to Strategy Analysis .................................................................................................... 54

6.5. Providing Water for Future Uses ................................................................................................ 57

6.5.1. Providing Water for Future Consumptive Uses through Contract Water from 

Canyon Ferry Reservoir and Lake Elwell.........................................................................................58

6.5.2. Providing Water for Future Municipal, Domestic, and Industrial Uses in the 

Gallatin Valley............................................................................................................................................64

6.6. System-Wide Water Management Strategies ...................................................................... 77

6.6.1. Increasing Canal and On-farm Irrigation Efficiencies................................................................77

6.6.2. Ecological Flow Releases from Canyon Ferry Reservoir and Lake Elwell ..........................86

6.7. Beaverhead River Basin Strategies ............................................................................................ 95

6.7.1. Decreasing the Drawdown for Clark Canyon Reservoir Flood Storage.............................95

6.7.2. Capping the Clark Canyon Reservoir Winter Release at 100 cfs ..........................................95

6.7.3. Decreasing Flood Storage and Capping Winter Releases.......................................................96

6.7.4. Performance and Trade-Offs for the Clark Canyon Reservoir 

Operational Strategies .......................................................................................................................................96

6.8. Sun River Basin Strategies ......................................................................................................... 101

6.8.1. Background and Objectives .............................................................................................................. 101

6.8.2. Increasing Willow Creek Feeder Canal Capacity ...................................................................... 105

6.8.3. New Off-Stream Storage for Sun River Water.......................................................................... 106

6.8.4. Increasing Pishkun Supply Canal Capacity ................................................................................. 107

6.8.5. New Off-Stream Storage with Increasing Pishkun Supply Canal Capacity................... 107

6.8.6. Performance and Trade-Offs for the Sun River Basin Strategies ...................................... 109

6.9. Musselshell River Basin Strategy ............................................................................................. 113

6.9.1. New Off-Stream Storage in the Lower Musselshell River Basin........................................ 113

6.10. Water Management Strategy for Increased Drought Resilience ............................. 119

6.10.1. Background ........................................................................................................................................... 119

6.10.2. Objectives............................................................................................................................................... 121

6.10.3. Performance.......................................................................................................................................... 123

6.11. Strategies Considered but not Evaluated ......................................................................... 130

6.11.1. Shift Drawdown Operations Timing at Canyon Ferry Reservoir and Lake Elwell..... 130

6.11.2. Beaverhead Valley Aquifer Recharge ......................................................................................... 130

6.11.3. Flushing Flow Releases from Clark Canyon Reservoir......................................................... 130

6.11.4. Musselshell River Basin Off-Stream Reservoir Fill Sequencing Change ...................... 131

7. Next Steps and Future Considerations ....................................................................133

7.1. Potential Future Applications of the Upper Missouri RiverWare 

Planning Model ..................................................................................................................... 134

7.2. Potential to Update Models ...................................................................................................... 134

7.3. Continued Collaboration and Support ................................................................................. 135

8. Uncertainty ................................................................................................................137

9. References..................................................................................................................139
Missouri Headwaters Basin Study

v 

Tables

Table 1.—Summary of Irrigated Areas by HUC8 Sub-Basin ................................................................................... 7

Table 2.—Summary of Reclamation Projects in the Missouri Headwaters Basin Study Area................... 7

Table 3.—Summary of State-Owned Reservoirs in the Missouri Headwaters Basin Study Area ..........10

Table 4.—Major Hydropower Facilities in the Missouri Headwaters ................................................................13

Table 5.—Preferred Minimum Instream Flows for Select Locations in the Missouri Headwaters ........19

Table 6.—Summary of Impacts Assessment Results by Region within the Study Area............................30

Table 7.—Local Meetings Attended during the Basin Study Process...............................................................35

Table 8.—Informational Meetings Held with Other Entities.................................................................................36

Table 10.—List of Evaluated Strategies..........................................................................................................................57

Table 11.—Future Developments Included in the Strategy ..................................................................................60

Table 12.—Projected Increases in Populations and Demands for the City of Bozeman and Other 

Communities and Rural Users in Gallatin County, Montana .......................................................65

Table 13.—Modeled Increases in Irrigation Efficiencies Compared to Baseline by Sub-basin.............79

Table 14.—Comparison of Irrigation Depletion Shortages for the Missouri Headwaters Upstream of 

Three Forks under the Increasing Canal and On-Farm Irrigation Efficiencies Strategy....80

Table 15.—Example Ecological Flow Release Scenarios Where Synchronized Releases 

were Modeled..................................................................................................................................................88

Table 16.—Clark Canyon Winter Release Guidelines...............................................................................................96

Table 17.—Modeled Reductions to Irrigation Shortages Associated with the Horse Creek 

Coulee Reservoir using Historical Streamflow Data..................................................................... 114

Table 18.—Summary of Flow Targets for the Big Hole River below Lake Creek at Wisdom Gage... 124

Figures

Figure 1.—Upper Missouri Basin Impacts Assessment and Missouri Headwaters Basin

Study process diagram. ................................................................................................................................. 3

Figure 2.—Missouri Headwaters Basin Study location map. .................................................................................. 5

Figure 3.—Irrigated lands in the Missouri Headwaters Basin study area.......................................................... 7

Figure 4.—Major water storage reservoirs in the study area. ..............................................................................11

Figure 5.—Hydropower facilities in the study area...................................................................................................14

Figure 6.—Normal range of flow for Missouri River compared to turbine capacity at 

Holter Dam. ......................................................................................................................................................16

Figure 7.—Missouri Headwaters Basin Study area population density. ..........................................................17

Figure 8.—Water rights closures in the Missouri Headwaters Basin study area. .........................................26

Figure 9.—Summary of Impacts Assessment results by region. .........................................................................29

Figure 10.—Components of the Missouri Headwaters Basin Study scenarios. ............................................46

Figure 11.—Overview of strategy locations.................................................................................................................55

Figure 12.—Resource benefit changes comparison chart for Providing Water for Future 

Consumptive Uses through Contract Water from Canyon Ferry Reservoir and

Lake Elwell strategy (2050s futures)......................................................................................................61

Figure 13.—Normal range of streamflow for the lower Gallatin River near Logan compared 

to senior Montana DFWP instream flow rates...................................................................................67

Figure 14.—Modeled depletions to surface water compared to aquifer recharge rates and 

outflows from recharge to surface water.............................................................................................69

Figure 15.—Modeled Canyon Ferry pipeline seasonal diversions for a sample two-year

sequence............................................................................................................................................................71

Figure 16.—Resource benefit changes comparison chart for the Providing Water for Future 

Municipal, Domestic, and Industrial Uses in the Gallatin Valley strategies 

(2050s futures).................................................................................................................................................75

Figure 17.—Montana irrigation trends (source data: USDA undated). ............................................................78
Contents

vi

Figure 18.—Resource benefit changes comparison chart for the Increasing Canal and 

On-farm Irrigation Efficiencies strategy (2050s futures)................................................................83

Figure 19.—Example of Canyon Ferry and Tiber Dams coordinated release scenario..............................88

Figure 20.—Example of a modeled ecological flow release based on 1956 conditions...........................90

Figure 21.—Comparison of number of ecological flow releases for each reservoir and 

combined flow releases under historical and future scenario conditions. ............................90

Figure 22.—Resource benefit changes comparison chart for the Ecological Flow Releases 

from Canyon Ferry Reservoir and Lake Elwell strategy (2050s futures). ................................. 93

Figure 23.—Modeled percent changes to Clark Canyon Water Supply Company and East 

Bench Irrigation District allocation fractions for a sample drought year sequence. .........98

Figure 24.—Resource benefit changes comparison chart for the Beaverhead River basin 

strategies (2050s futures). ..........................................................................................................................99

Figure 25.—Map of the Sun River basin showing major hydrologic features, irrigation 

districts, and flow monitoring stations. ............................................................................................. 103

Figure 26.—Modeled Willow Creek end of water year storage for the increased WCFC 

capacity strategy for the worst case paleohydrology scenario compared to 

baseline conditions. ................................................................................................................................... 106

Figure 27.—Modeled irrigation depletion shortages to GID considering additional off-stream 

storage strategy and additional off-stream storage strategy with an increase in 

Pishkun Supply Canal capacity for the worst case paleohydrology scenario 

compared to baseline conditions......................................................................................................... 108

Figure 28.—Modeled average percent full additional 30,000 acre-feet of off-stream storage 

would be with and without a modeled increase in capacity of the Pishkun 

Supply Canal, including historical and future 2050s scenarios as well as extreme 

paleo events. ................................................................................................................................................. 108

Figure 29.—Resource benefit changes comparison chart for the Sun River basin strategies 

(2050s futures).............................................................................................................................................. 111

Figure 30.—Modeled Horse Creek Coulee Reservoir storage for 1950 - 2010 historical period....... 116

Figure 31.—Resource benefit changes comparison chart for the Musselshell River basin 

strategy (2050s futures)............................................................................................................................ 117

Figure 32.—Droughts in the Missouri Headwaters during the last 1,200 years........................................ 120

Figure 33.—Modeled flows for Big Hole River near Wisdom gage compared to the

historical gaged flow................................................................................................................................ 125

Figure 34.—Resource comparison grid for Water Management Strategy for Increased 

Drought Resilience strategy. (2050s futures). ................................................................................. 127
Missouri Headwaters Basin Study

1 

1. Introduction 

Through the WaterSMART1 program, the Bureau of Reclamation (Reclamation) 

is working with external partners to understand and address current and future 

risks to water resources in the Western United States. Reclamation, in partnership 

with the Montana Department of Natural Resources and Conservation (Montana 

DNRC) and with support from the U.S. Geological Survey (USGS), conducted 

the Upper Missouri Basin Impacts Assessment (Impacts Assessment) and 

Missouri Headwaters Basin Study (Basin Study) to evaluate risks in the Upper 

Missouri River basin upstream of Fort Peck Reservoir. This region includes the 

Upper Missouri and the Musselshell Rivers. In addition to serving as the 

headwaters to much of the nation, these watersheds support habitats for numerous 

fish and wildlife species and supply water for agriculture, hydropower, recreation, 

and tribal, municipal, industrial, and domestic uses. The Upper Missouri River 

and Musselshell River basins together encompass a drainage area of about 

50,000 square miles. They are the primary water source for 320,000 people and 

approximately 1.1 million acres of irrigated land. Topography ranges from high 

Rocky Mountain peaks in Glacier National Park to rolling plains in central and 

eastern Montana, with corresponding elevations ranging from approximately 

2,200 feet to 11,000 feet above mean sea level (msl). 

The Impacts Assessment (Reclamation 2019a) provides foundational information 

on historical and projected future water supply and demand and potential risks to 

future water supplies. This Basin Study uses this information on future water 

supply, demand, and risks, along with modeling tools developed as part of the 

Impacts Assessment, to identify and evaluate strategies for alleviating potential 

future risks to water resources in the study area. This report presents results from 

the Basin Study, with a focus on the identification and analysis of strategies for 

alleviating potential risks to water supplies through improved management and 

reducing demands. 

1.1. Basin Study Purposes and Objectives

The purpose of the Basin Study is to develop and evaluate strategies for

addressing water resource challenges under a range of potential future conditions, 

including population growth, changes in future water supply and demand related 

to climate change, and supply conditions based on a broad range of historical 

conditions drawn from paleohydrology analysis. Strategies were developed in 

coordination with watershed groups and other stakeholders to address challenges 

identified in the Impacts Assessment. These strategies include alternative 

management and operating policies, as well as construction of new water 

resources infrastructure and modification of existing infrastructure. Strategies are 

1 Water Sustain and Manage America’s Resources for Tomorrow. 
1. Introduction

2 

evaluated by considering their effects on five resource categories—water 

deliveries, hydroelectric power resources, flood control operations, ecological 

resources (including water quality, fish and wildlife habitat, and Endangered 

Species Act [ESA] listed species), and recreation. 

The Basin Study was conducted for a variety of reasons. First, the 2015 Montana 

State Water Plan directed Montana DNRC to plan for future management of water 

in the Missouri Headwaters given population and economic growth and changing 

water supplies and demands. Also, previous studies, including the Reclamation 

SECURE Water Act1 Report to Congress (Reclamation 2021) and the Impacts 

Assessment (Reclamation 2019a), identified potential changes in future 

conditions that highlight the need for a long-term planning study. Specifically, a 

future warming trend and changes in spring runoff volume and timing are 

projected. Evapotranspiration and associated crop demand as well as reservoir 

evaporation are also projected to increase with warming temperatures. Projected 

changes in runoff timing in the snowmelt dominated watersheds of the Missouri 

Headwaters are likely to have a significant effect on the timing of streamflow for

irrigation and municipal demands. Projected changes in runoff timing and volume 

are also likely to impact the amount and timing of water available for fish, 

wildlife, and recreation, which have become an important component of the 

region’s economy. Reclamation’s storage reservoirs in the study area may play an 

even larger role meeting the region’s water management objectives in the future 

with warmer temperatures increasing demand for stored water and higher annual 

runoff volume along with earlier spring runoff possibly increasing the need for 

flood control storage. 

Finally, because much of the Missouri Headwaters area is closed to most new 

surface water appropriation, groundwater may be increasingly used to meet water 

demands in the future. However, new groundwater uses are complicated by the 

interaction between surface and groundwater. Aquifer recharge, return flow 

patterns, and discharge from aquifers to streams are likely to change with 

increasing demands and more efficient irrigation. 

The Basin Study seeks to address the needs identified above by achieving the 

following objectives. 

• Assess current and projected future water supply; this study focuses on use 

of information characterizing the distant past (paleo), the recent past 

(historical), and projected future conditions. 

• Assess current and projected future water demand; this study includes, but 

is not limited to, existing information related to groundwater sources in 

high-demand areas, such as the Gallatin and Beaverhead valleys.

1 Science and Engineering to Comprehensively Understand and Responsibly Enhance (SECURE) 

Water Act (Public Law 111-11, Subtitle F of Title IX, §9501 – §9510)
Missouri Headwaters Basin Study

3 

• Evaluate water supply risks by analyzing simulated performance of water 

and power infrastructure and operations under paleo, historical, and future 

hydrology scenarios. 

• Identify and evaluate potential strategies that may reduce any imbalances; 

development and evaluation of strategies includes outreach and 

involvement by stakeholders. 

As previously mentioned, this Basin Study builds on the Impacts Assessment 

(Reclamation 2019a) that Reclamation also conducted in partnership with

Montana DNRC. Additionally, USGS provided guidance and technical support 

for the Impacts Assessment by developing paleo reconstructed streamflow 

records, which Reclamation used to develop paleohydrology streamflow scenarios 

for the study. Figure 1 depicts how the Impacts Assessment and Basin Study are 

interrelated, with the Impacts Assessment (blue) focused on assessing water 

supply and demand and evaluating future risks to water supplies, and the Basin 

Study (brown) focused on identifying and evaluating potential strategies in 

collaboration with basin stakeholders. 

Figure 1.—Upper Missouri Basin Impacts Assessment and Missouri Headwaters Basin 

Study process diagram.
1. Introduction

4 

The datasets, models, and information generated for the Impacts Assessment and 

Basin Study provide a foundation for future investigations and implementation of 

strategies. The partnerships developed between Reclamation, Montana DNRC, 

and local stakeholders will also facilitate future planning efforts. 

1.2. Location and Description of the Missouri 

Headwaters Study Area

This Missouri Headwaters Basin Study area encompasses the Upper Missouri 

River and Musselshell River basins upstream of Fort Peck Reservoir (Figure 2). 

The study area covers about 50,000 square miles, and the watershed outflow 

averages about 6.7 million acre-feet annually. 

The Missouri River begins in the Rocky Mountains of southwestern Montana 

where the drainages for the Jefferson, Madison, and Gallatin Rivers join to form 

the Missouri River near the town of Three Forks. These drainages include a series 

of mountain ranges with peaks that approach 12,000 feet, and intermountain 

valleys with elevations of 4,000 to 6,000 feet. Along the Continental Divide to the 

north, the Sun River joins the Missouri River in the city of Great Falls, while the 

Teton, and Marias Rivers join the Missouri River near Fort Benton. The study 

area also encompasses central Montana watersheds, including the Smith and 

Judith Rivers (generally ranging from 3,000 feet to 6,000 feet), and the extensive 

tributary drainage of the Musselshell River (ranging from about 2,000 to 

5,000 feet). 

The downstream-most gaging stations in the study area are USGS Musselshell 

River at Mosby gaging station (#06127500) for the Musselshell River basin 

portion of the study area and USGS Missouri River at Landusky gaging station 

(#06115200) for the remainder of the study area. At the downstream end of the 

study area, the Missouri River and Musselshell River flow into Fort Peck 

Reservoir (at about elevation 2,250 feet msl). Fort Peck Reservoir is the first of a 

series of major Missouri River main-stem reservoirs managed primarily by the 

U.S. Army Corps of Engineers (USACE) for flood control. This study focuses on 

the watersheds upstream of Fort Peck Reservoir and including water supply 

reservoirs managed by Montana DNRC and Reclamation, not the collectively 

managed Missouri River main-stem reservoirs.
Missouri Headwaters Basin Study

5 

Figure 2.—Missouri Headwaters Basin Study location map.
1. Introduction

6 

1.3. Water Use and Development

This section describes water uses and water resources development in the study 

area. Water uses in the study area include consumptive uses such as irrigation and 

municipal use as well as non-consumptive uses such as hydropower and instream 

flow for fisheries. This section also describes the major infrastructure that is used 

to regulate, manage, and deliver surface water to users throughout the study area. 

1.3.1. Irrigation

Irrigation is by far the largest 

consumptive use in the study 

area. The study area 

encompasses about 1.1 million 

irrigated acres, mostly for 

livestock forage and small 

grains. Primary irrigated crops 

include alfalfa, pasture grass, 

other hay crops, and grains 

such as wheat, barley, and corn. 

Surface water supplies over 97 percent of irrigation water (Montana DNRC

2014). As described in the Impact Assessment, the Montana DNRC inventoried 

irrigated lands for the 2015 State Water Plan (Montana DNRC 2014) and refined 

those estimates for the Impacts Assessment and Basin Study. Irrigated acreage 

within the study area is summarized by Hydrologic Unit Code eight-digit level 

drainage areas (HUC8 sub-basins) in Table 1 and depicted in Figure 3. 

Federal Irrigation Projects and Reservoirs

The study area encompasses several Federal irrigation projects, including five 

units of the Pick-Sloan Missouri Basin Program (PSMBP) as well as the Sun 

River Project. The PSMBP supplies irrigation water to about 20 percent of the 

irrigated lands within the study area. The Sun River Project, which was authorized 

prior to PSMBP, encompasses additional irrigation units which comprise about 

10 percent of the study area’s irrigated lands. These projects and features are 

summarized in Table 2. Canyon Ferry Reservoir, part of the Canyon Ferry Unit of 

PSMBP, also stores and releases water to mitigate impacts of irrigation 

withdrawals and crop water consumption on downstream hydropower water 

rights. This mitigation of impacts on downstream water rights makes reliable 

irrigation possible for a substantial amount of agricultural land in the headwaters. 

Irrigation in the Helena Valley. Irrigation in the Helena Valley.
Missouri Headwaters Basin Study

7 

Table 1.—Summary of Irrigated Areas by HUC8 Sub-Basin

HUC-8 HUC-8 Name Area

(acres) HUC-8 HUC-8 Name Area(acres) 

10020001 Red Rock 65,491 10030105 Belt 37,299

10020002 Beaverhead 77,566 10030201 Two Medicine 8,244

10020003 Ruby 37,590 10030202 Cut Bank 22,945

10020004 Big Hole 150,396 10030203 Marias 90,315

10020005 Jefferson 51,402 10030204 Willow 2,333

10020006 Boulder 10,530 10030205 Teton 47,190

10020007 Madison 33,392 10040103 Judith 17,031

10020008 Gallatin 102,208 10040201 Upper Musselshell 60,503

10030101 Upper Missouri 67,789 10040202 Middle Musselshell 16,956

10030102 Upper MissouriDearborn17,386 10040203 Flatwillow 14,819

10030103 Smith 34,632 10040204 Box Elder 7,756

10030104 Sun 135,531 10040205 Lower Musselshell 5,230

Total irrigated acreage within study area: 1,114,534 acres.

Figure 3.—Irrigated lands in the Missouri Headwaters Basin study area. 
1. Introduction

8 

Project/Program Unit Purpose and Associated Water 

Source

Pick-Sloan 

Missouri Basin 

Program 

(PSMBP) 

East Bench Unit Irrigation deliveries for 56,000 acres 

from Clark Canyon Reservoir on the 

Beaverhead River

Crow Creek Pump Unit Irrigation deliveries for 23,400 acres 

from the Mainstem Missouri River near 

Toston

Canyon Ferry Unit Multi-purpose deliveries from the 

Mainstem Missouri River near Canyon 

Ferry Reservoir; hydropower 

generation

Helena Valley Unit Irrigation deliveries for 17,000 acres 

and municipal and industrial deliveries 

for City of Helena from the Mainstem 

Missouri River and Lake Helena

Lower Marias Unit Irrigation deliveries for up to 127,000 

acres (ultimately not developed) from 

Lake Elwell; currently this unit meets 

flood control, recreation, fish and 

wildlife, and municipal and industrial 

water supply needs

Sun River 

Project 

Gibson Reservoir, 

Pishkun and Willow 

Creek Dikes

Irrigation deliveries for 93,000 acres 

from Sun River from Gibson, Pishkun, 

and Willow Creek Reservoirs

Table 2.—Summary of Reclamation Projects in the Missouri Headwaters Basin Study Area
Missouri Headwaters Basin Study

9 

 

Nine

State-Owned Storage Reservoirs

state-owned 

dams and reservoirs 

provide full service 

and supplemental 

irrigation water 

supplies and underpin 

flow management in 

some watersheds. 

State-owned dams that 

store irrigation water 

are listed in Table 3. 

Montana DNRC also 

owns and operates the 

Toston Dam on the 

Missouri River just 

upstream of Canyon 

Ferry Reservoir. 

Although Toston Dam 

is a run-of-river facility,

1 it provides about 29,200 acre-feet of water for irrigation 

annually through the Broadwater-Missouri Canal. The reservoirs also provide 

recreational benefits.

Figure 4 shows the locations of the major water storage reservoirs in the study 

area, including the Federal, State, and privately-owned reservoirs. Privatelyowned reservoirs primarily supply water for irrigation. Privately-owned reservoirs 

are not discussed in detail in this report but include: Swift Reservoir, Lake 

Frances, Bynum Reservoir, Eureka Reservoir, Whitetail Reservoir, Lima 

Reservoir, Petrolia Reservoir, and Newlan Creek Reservoir. 

1 A run-of-river facility operates on the flow of the river and has very little storage capacity in the 

reservoir behind the dam.

Ruby Reservoir.
1. Introduction

10

Table 3.—Summary of State-Owned Reservoirs in the Missouri Headwaters Basin Study 

Area

Reservoir Source(s)

Active 

Storage

(acre-feet) 

Approximate 

Acres Irrigated*

Ruby Reservoir Ruby River 37,611 33,000

Middle Creek Reservoir

(Hyalite Lake)

West and East 

Hyalite Creeks

10,184 16,000**

Willow Creek Reservoir Willow Creek 

Dry Hollow Creek 

Norwegian Creek

18,000 12,950

Lake Sutherlin North Fork Smith 

River

11,528 12,095

Nilan Reservoir Smith Creek

Ford Creek

10,092 10,000

Ackley Lake Judith River 5,721 5,000

Bair Reservoir North Fork 

Musselshell River

7,300 35,000***

Martinsdale Reservoir South Fork 

Musselshell River

23,348 -

Deadman’s Basin 

Reservoir 

Musselshell River 72,218 30,000

*Includes full-service and supplemental acres

**Hyalite Lake also supplies up to 5,900 acre-feet of water for City of Bozeman. 

***Bair and Martinsdale Reservoirs work in conjunction with each other to irrigate a combined 

 total of 35,000 acres. 
Missouri Headwaters Basin Study

11

Figure 4.—Major water storage reservoirs in the study area.
1. Introduction

12

1.3.2. Hydropower Facilities

Table 4 summarizes the 

major hydropower facilities 

in the Missouri Headwaters, 

listed from upstream to 

downstream. Hydropower 

facilities in the study area 

have a combined capacity of 

400.5 megawatts (MW). 

The upstream-most 

hydropower facility on the 

Missouri River mainstem is 

at Montana DNRC’s Toston 

Dam, which contains the 

Broadwater Power Facility, 

a 10-MW, run-of-the-river facility. 

Black Eagle Dam at Great Falls, Montana.

Toston Dam is just upstream of Canyon Ferry 

Reservoir. Hydropower facilities at Reclamation’s Canyon Ferry Dam have a 

generation capacity of 50 MW. Facilities at Canyon Ferry Dam also include a 

single mechanical turbine that pumps water to the Helena Valley Reservoir but 

does not produce electricity. Tiber Dam has a privately-owned hydropower 

facility built in 2004, but Tiber Dam operational procedures are not altered for 

power generation objectives. 

The remaining hydropower facilities within the study area are owned and 

operated by NorthWestern Energy. NorthWestern Energy’s Missouri-Madison 

Project is upstream of Canyon Ferry Reservoir. This project includes the Madison 

Plant on the Madison River near Ennis, Montana. The Madison Plant is operated 

in conjunction with Hebgen Lake, which is near the Madison River headwaters 

and stores and releases water for the project. The remaining seven NorthWestern 

Energy projects are on the Missouri River downstream of Canyon Ferry Reservoir 

(Figure 5). 
Missouri Headwaters Basin Study

13

Table 4.—Major Hydropower Facilities in the Missouri Headwaters

Dam Stream

Hydraulic 

Capacity*

(cfs)

Generating 

Capacity 

(MW)

Owner or Operator

Madison Madison River 1,650 8 NorthWestern 

Energy

Toston Missouri River 7,200 10 Montana DNRC

Canyon Ferry Missouri River 6,390 50 Reclamation

Hauser Missouri River 4,740 19 NorthWestern 

Energy

Holter Missouri River 7,100 48 NorthWestern 

Energy

Black Eagle Missouri River 5,040 21 NorthWestern 

Energy

Rainbow Missouri River 8,000 60 NorthWestern 

Energy

Cochrane Missouri River 10,000 69 NorthWestern 

Energy

Ryan Missouri River 5,900 60 NorthWestern 

Energy

Morony Missouri River 8,280 48 NorthWestern 

Energy

Tiber Marias River 7.5 Tiber-Montana LLC

Total 400.5

*Based on water rights filings

cfs = cubic feet per second
1. Introduction

14

Figure 5.—Hydropower facilities in the study area.
Missouri Headwaters Basin Study

15

Canyon Ferry hydropower operations are primarily governed by the Missouri 

River Coordination Agreement (Reclamation and Montana Power Company 

1972). NorthWestern Energy projects are also operated in accordance with the 

Missouri River Coordination Agreement, and in accordance with provisions and 

requirements specified in the Federal Energy Regulatory Commission (FERC) 

license for the Missouri-Madison Project (Hydropower Reform Coalition and 

River Management Society 2014). Objectives of the Missouri River Coordination 

Agreement include:

• Maximize power generation benefits for both Canyon Ferry and the 

downstream Northwestern Energy hydropower facilities 

• Provide irrigation and municipal and industrial (M&I) water supply 

• Provide flows for fish, wildlife, and recreational use

• Manage flows for flood control 

• Prevent ice-jam flooding above Canyon Ferry 

During median and drier years, the larger dams have the capacity and water rights 

to generate electricity with the entire flow of the river during all months in most 

years except May and June. The water rights for some of the larger-capacity 

facilities have relatively early priority dates and can effectively limit the flow 

available for junior water rights holders. A Montana DNRC water availability 

analysis (Montana DNRC 1981) found that water might only be available for 

storage, diversion, and use during spring runoff in 60 percent of years. The study 

further found that due to the senior water rights for some larger-capacity 

hydropower facilities, water is seldom available for storage, diversion, and use 

after August 9 until early spring of the next year. 

Figure 6 is a comparison of observed streamflow for the Missouri River below 

Holter gaging station (USGS station number 06066500) and the turbine capacity 

for the Holter Dam hydropower facility. The Holter Dam hydropower facility has 

a right to use all flow up to the turbine capacity. When streamflow falls below the 

turbine capacity, then flow to junior water users upstream is curtailed. Note that 

during most years (the middle year line and below), the flow is only above the 

turbine capacity for a short time during spring runoff. 
1. Introduction

16

Figure 6.—Normal range of flow for Missouri River compared to turbine capacity at Holter 

Dam.

1.3.3. Municipal and Domestic

The Missouri River and its tributaries 

in the study area are the primary water 

source for about 318,000 people 

(Montana DNRC 2014). Much of the 

population live in Gallatin, Madison, 

and Lewis and Clark counties in the 

southwestern portions of the study area 

(Figure 7). These counties have been 

growing rapidly over the past 20 years 

and this growth is expected to 

continue. Larger communities, 

including Bozeman, Helena, and Great 

Falls, rely on surface water sources for 

most of their supply. Smaller 

communities and rural populations 

more commonly use groundwater 

sources for their supply. 

Housing development in the Helena Valley.
Missouri Headwaters Basin Study

17

Figure 7.—Missouri Headwaters Basin Study area population density. 

1.3.4. Environment

The study area includes the 

Missouri Headwaters blueribbon trout fisheries of the 

Big Hole, Gallatin, 

Beaverhead, Jefferson, 

Madison, Smith, and 

Missouri Rivers. The Upper 

Missouri River and its 

reservoirs provide some of 

the highest value recreation 

areas in the state. Federal 

and State-owned reservoirs

provide much of the flatwater recreational 

opportunities, with Canyon 

Ferry Reservoir ranking number one in a recent survey of lakes and reservoirs in 

Montana. The Missouri River between Holter Dam and Cascade and the Madison 

River rank second and third respectively amongst Montana streams for 

recreational use (Montana Department of Fish, Wildlife and Parks 

[Montana DFWP] 2013). 

Upper Missouri River, National Wild and Scenic portion.
1. Introduction

18

The Upper Missouri River basin also offers other water-dependent recreational 

activities which are likely to be affected by changes in hydrology and/or water 

management and operations, such as fishing, white-water rafting, reservoir 

boating, camping, swimming, nature study, and hunting. Downstream, the 

Missouri National Wild and Scenic River in the lower portion of the study area is 

a common destination for recreational floaters and boaters. Changes in the 

hydrologic regime and reservoir operations may alter the timing of boat ramp 

availability and flows associated with floating rivers. 

Instre

Montana DFW

am Flow

P holds instream flow rights within the Upper Missouri River basin

for fish, wildlife, and aquatic habitat. The major rights fall under two general 

categories: 

1) Murphy Rights. In 1969, the Montana legislature enacted a law allowing 

the Montana Fish and Game Commission to file for water rights on the 

unappropriated waters of 12 streams to maintain stream flows necessary 

for the preservation of fish and wildlife habitat (Section 89-901 (2), 

Revised Codes of Montana [RCM] 1947). In the Missouri Headwaters, 

Montana DFWP filed for Murphy Rights for the Madison, Gallatin, West 

Gallatin, Missouri and Smith Rivers, and Big Spring Creek. These rights 

have December 1970 priority dates. 

2) Water Reservations. In 1992, Montana DFWP was granted water 

reservations for minimum instream flows for 245 streams or stream 

reaches in the study area to protect fisheries, aquatic habitat, and 

associated recreational values. In the Missouri River Headwaters, instream 

reservations generally were based on the amount of instream flow required 

to protect riffle habitat in the streams as quantified by the Wetted 

Perimeter Inflection Point method (Montana DFWP 1989). By §85-2-316 

Montana Code Annotated (MCA) these rights were limited by statute to 

one-half the average annual flow for gaged streams. 

For the Basin Study, the greater of either Murphy Rights or Water Reservations 

were used to characterize instream flow objectives and as metrics for 

characterizing changes to instream flow at key locations in the Missouri 

Headwaters. These locations and instream flow rates are summarized in Table 5

with rates based on Murphy Rights shaded in grey. 
Missouri Headwaters Basin Study

19

Table 5.—Preferred Minimum Instream Flows for Select Locations in the Missouri Headwaters

River Basin Location Flow 

(cfs) Period River Basin Location Flow (cfs) Period

Beaverhead River 

basin

Upper Beaverhead River 200 annual Missouri River 

Mainstem

Upper Missouri River 1,500 Jan 1 - Jan 31

Lower Beaverhead River 200 annual Upper Missouri River 3,000 Feb 1 - May 15

Red Rock River 60 annual Upper Missouri River 4,000 May 16 - Jun 

30

Big Hole River basin Lower Big Hole River 573 annual Upper Missouri River 3,816 Jul 1 - Jul 15

Upper Big Hole River 160 annual Upper Missouri River 1,500 Jul 16 - Sep 14

Gallatin River basin Upper Gallatin River 800 May 16 - Jul 15 Upper Missouri River 3,000 Sep 15 - Dec 

31

Upper Gallatin River 400 Jul 16 - May 15 Middle Missouri River 3,327 annual

East Gallatin River 170 annual Lower Missouri River 4,652 annual

Lower Gallatin River 947 May 1 - May 15 Dearborn River 110 annual

Lower Gallatin River 1,278 May 16 - May 

31

Musselshell River basin Upper Musselshell River 80 annual

Lower Gallatin River 1,500 Jun 1 - Jun 15 Middle Musselshell River 80 annual

Lower Gallatin River 1,176 Jun 16 - Jun 30 Lower Musselshell River 70 annual

Lower Gallatin River 850 Jul 1 - Aug 31 Musselshell River at 

Mosby

70 annual

Lower Gallatin River 800 Sep 1 - Apr 30 Ruby River basin Ruby River below 

Reservoir

40 annual

Jefferson River basin Upper Jefferson River 50 annual Ruby River near mouth 40 annual

Lower Jefferson River 1,095.5 annual Smith River basin Lower Smith River 372 May 1 - May

15

Boulder River 47 annual Lower Smith River 400 May 16 - Jun 

15

Judith River basin Upper Judith River 25 annual Lower Smith River 398 Jun 16 - Jun 30

Lower Judith River 160 annual Lower Smith River 150 Jul 1 - Apr 30
1. Introduction

20

Table 5.—Preferred Minimum Instream Flows for Select Locations in the Missouri Headwaters

River Basin Location Flow 

(cfs) Period River Basin Location Flow (cfs) Period

Madison River basin Madison River below Ennis 

Lake

825 annual Upper Smith River 150 May 5 - Jun 30

Madison River below Ennis 

Lake

1,200 Jan 1 - May 31 Upper Smith River 90 Jul 1 - Apr 30

Madison River below Ennis 

Lake

1,500 Jun 1 - Jun 30 Sun River basin Upper Sun River 100 annual

Madison River below Ennis 

Lake

1,423 Jul 1 - Jul 15 Middle Sun River 130 annual

Madison River below Ennis 

Lake

1,300 Jul 16- Dec 31 Lower Sun River 130 annual

Marias River basin Birch Creek 10 annual Teton River basin Upper Teton River 35 annual

Upper Marias River 200 annual

Lower Marias River 488.5 annual

Rates based on Murphy Rights are shaded in grey. All other rights are based on water reservations.
Missouri Headwaters Basin Study

21

Fish Species of 

Concern 

Pallid sturgeon inhabit the 

Missouri River between the 

mouth of the Marias River 

and Fort Peck Reservoir and 

have been listed as 

endangered by the U.S. Fish 

and Wildlife Service 

(USFWS). Currently, the 

pallid sturgeon is the only 

federally-listed fish species 

under the ESA within the 

study area. Montana 

designated the pallid sturgeon 

with the second highest rank on the Global Conservation Status, G2,1

 and highest 

rank on the Montana Species Ranking Codes scale S1,2 on the internationally 

recognized system for ranking rare, threatened and endangered species throughout 

the world. According to the 2014 Revised Recovery Plan, the overall status of the 

species has improved since the original 1990 listing and is currently stable, 

although population estimates of wild pallid sturgeon within some reaches of the 

Missouri River indicate that wild populations may be declining or extirpated. 

The last fluvial Arctic grayling 

population in the contiguous 

United States resides in the Big 

Hole River basin of the study 

area. This Arctic grayling 

population is genetically 

distinct from those in Alaska 

and Canada (Cayer and 

McCullough 2013). Due to 

declining numbers, the USFWS was petitioned in 1991 to list this grayling 

population under the ESA. Throughout the 1990s and early 2000s, an ESA listing 

of Arctic grayling was considered warranted, but precluded. In 2014, the USFWS 

found that this distinct population segment in the Upper Missouri River basin 

does not warrant protection under the ESA, due largely to significant conservation 

efforts in the past decade. (USFWS 2014). Led by the multi-agency Arctic 

1 G2 is imperiled—At high risk of extinction due to very restricted range, very few populations 

(often 20 or fewer), steep declines, or other factors. See the ranking at 

http://explorer.natureserve.org/granks.htm. 

2 S1 is at high risk because of extremely limited and/or rapidly declining population numbers, 

range and/or habitat, making it highly vulnerable to global extinction or extirpation in the state. 

See ranking at http://fieldguide.mt.gov/statusCodes.aspx. 

Arctic grayling. 

Courtesy of USFWS. 

Pallid sturgeon.

Photo by Hagerty Ryan. Courtesy of USFWS. 
1. Introduction

22

Grayling Recovery Program, these conservation efforts include habitat protection 

and restoration, and reintroduction and recolonization. A drought action plan for 

the Big Hole River has been a part of this effort. Restoration and reintroduction 

areas include the Red Rock River and Red Rock Lakes National Wildlife Refuge, 

the Ruby River, and the North and South Forks of the Sun River. 

1.4. Groundwater Resources

Wells and springs in the study area yield water from aquifers in shallow alluvium, 

deeper semi-consolidated to consolidated basin-fill sediments, and bedrock. They 

may be recharged by direct infiltration of precipitation, leakage from irrigation 

ditches, irrigation return flows, and seepage from streams. 

Alluvial aquifers are by far the most common sources of groundwater for 

irrigation, municipal, industrial, household, and livestock purposes. They exist 

along floodplains of major streams. These aquifers are typically less than 100 feet 

thick and therefore, are accessible by shallow wells at relatively low expense and 

have hydraulic properties favorable to groundwater production. 

Aquifers in the plains portion of the Upper Missouri River basin include thin 

surficial sediments that overlie bedrock and top benches. The Greenfields Bench 

and Burton Bench terrace aquifers have relatively high permeability and are the 

primary sources of water for domestic and public water supply use in the area. 

They are both primarily recharged by irrigation water. 

Groundwater within bedrock aquifers in the study area occurs in discontinuous 

fractures and faults in sandstone, siltstone, shale, and carbonate rocks. The most 

productive bedrock aquifer in the basin is the Madison Group aquifer which is 

especially important in the City of Great Falls area and is the source of Lyman 

Springs, which is an important municipal water source for the City of Bozeman. 

On a regional scale, groundwater in the bedrock often is in hydraulic 

communication with alluvial aquifers and discharge in topographically lower 

areas by upward leakage to shallower aquifers and streams. 

The Basin Study incorporates groundwater contributions to surface water based 

on previous studies of the regions aquifers from the Montana Bureau of Mines 

and Geology (MBMG), USGS, and other sources. Details of how groundwater 

contributions to surface water were quantified in different parts of the study area 

are discussed in the Impacts Assessment, Reclamation (2019a).
Missouri Headwaters Basin Study

23

2. Characterization of Historical and 

Projected Future Conditions

This section summarizes historical and projected future water supply and demand 

in the study area and impacts of projected changes in hydrology and population 

on water resources management and operations within the study area. Water 

supply, demand, and potential risks to future water supplies were analyzed and 

documented in the Impacts Assessment (Reclamation 2019a). Results of the 

Impacts Assessment were subsequently used to identify and evaluate strategies in 

the Basin Study. 

This summary provides foundational information for the discussion and 

evaluation of strategies that were developed to alleviate the impacts of potential 

future supply and demand scenarios. As part of the discussion of historical water 

supply and demand, observed droughts occurring in the last one hundred years or 

so help to identify areas where water shortages were particularly severe. 

Conversely, observed pluvial (wet) periods help to identify where flooding and 

other associated impacts (e.g., loss of hydropower production due to spilling) may 

be an issue.

2.1. Historical Challenges and Considerations

In the Impacts Assessment, historical water supply and demand were evaluated 

over the 50-year period from 1950 to 1999 (termed the historical scenario). Daily 

average temperatures in the study area increased by about 1.4 degrees Fahrenheit 

(°F) over the historical scenario; however, average annual precipitation did not 

exhibit a significant trend. Average snowpack on April 1, which is an indicator of 

seasonal snowmelt runoff, decreased during this period, corresponding with 

observed warming. Thus, the volume of annual runoff has not changed, but the 

timing of snowmelt and seasonal runoff peak has shifted toward earlier in the 

year. 

Most of consumptive water demands in the Upper Missouri River basin have 

historically been agricultural water use, comprising about 85 percent of the total 

consumptive use, or about 1.7 million acre-feet per year. Reservoir evaporation 

comprises about 12 percent of the total consumptive use, while M&I use 

comprises just one percent of the total consumptive use. Most of the agricultural 

lands are within the valleys of river basins, while precipitation falls primarily in 

the mountainous headwaters of the study area, resulting in reliance on the regions 

snowpack and storage reservoirs for water supply. 
2. Characterization of Historical and Projected Future Conditions

24

Meeting the needs of various water users in the study area has historically been a 

challenge due to variability in climate in addition to long-term climate changes. 

The Dust Bowl Drought, which lasted from 1929 to 1943 (15 years) was the 

drought of record1 for the Missouri River basin draining to Fort Benton. The late 

century drought from about 1985 to 1992 was almost as severe and part of more 

recent management memory. The Millennium Drought from 2000 to 2010 was the 

drought of record for the Musselshell River basin draining to Mosby. On many 

Upper Missouri River tributaries, during these droughts, irrigation demands have 

exceeded the late-summer water supply, and this has led to stream dewatering. In 

1988, both the Big Hole and Jefferson Rivers were dewatered to meet irrigation 

demands and at the time there were no minimum instream flow requirements. The 

historical scenario period used was limited by naturalized streamflow data 

availability and consequently does not include either the Dust Bowl Drought 

(before the period in the 1930s) or the Millennium Drought (after the period in the 

2000s). In some instances, to provide context to simulated historical conditions, 

the historical scenario flows are compared to observed conditions during these 

two droughts of record. 

Some adaptation to historical changes in water supply and demand related to 

warming, as well as changes in the timing and duration of droughts and wet 

periods, have already been occurring within the study area. Some examples 

include modification of crop planting or harvest dates. 

Water managers and farmers consider uncertain future conditions. Use of 

paleohydrology data, such as in the form of tree rings analyses, can provide 

additional historical context to existing conditions and may factor into operational 

or planning decisions. The Impacts Assessment analyzed tree rings and other data 

to examine conditions from 1100 - 1950 Common Era (CE) as well as analyzing 

the historical record. The paleohydrology analysis included extreme events: the 

Most Intense Drought (MID), Most Intense Pluvial (MIP), Longest Drought (LD), 

Longest Pluvial (LP). The historical record included severe droughts: the Dust 

Bowl Drought, the Mid-Century Drought of the 1950s, and the Millennium 

Drought. This analysis showed that the range in annual streamflow over the last 

900 years is greater than the range over the historical scenario period. This is to be 

expected, in part because of the larger number of years contributing to the range. 

1 Drought of record is defined as the worst recorded drought since compilation of historical 

hydrologic data began in the region in the late 19th century.
Missouri Headwaters Basin Study

25

2.1.1. Population Growth

Montana has a growing population, and much of this growth is occurring in a few 

concentrated areas in the Missouri Headwaters study area, such as the Gallatin 

Valley. Communities in the headwaters already face challenges in providing 

water for a growing population because most of the flow in the basin has been 

appropriated for irrigation, hydropower, and municipal uses along with instream 

flows needed to support fisheries and recreation. Rural water users in Gallatin 

Valley and other areas have increasingly relied on groundwater sources to meet 

demands. 

2.1.2. Closed to Further Water Appropriations

In 1993, due to large senior hydropower rights and late-season water shortages on 

tributaries, the Montana Legislature closed the Missouri River drainage above the 

Great Falls, including all tributaries, to further appropriations of water, with some 

exceptions for groundwater, storage of high spring flow, and domestic, municipal 

and stock use (§85-2-343, MCA) (Figure 8). A similar, overlapping closure is 

specific to the Jefferson and Madison River basins (§85-2-341, MCA). The Teton 

River basin below the Great Falls is also closed to most new appropriations 

(§85-2-330, MCA). There is an administrative closure on the North and South 

Forks of the Musselshell River, and the Musselshell River downstream to the 

mouth of Flatwillow Creek that applies to consumptive uses during the period 

July 1 through August 31 (36.12.1016, Administrative Rules of Montana [ARM]). 

Stipulations in the Upper Missouri Wild and Scenic Compact will close much of 

the lower portion of the study area to new appropriations when designated 

volumes available for new depletion are reached (§85-20-501, MCA). 

The basin closures create administrative constraints that emphasize the need for 

additional data and modeling of historical and future water supply and demand, 

which was done as part of the Impacts Assessment (Reclamation 2019a).
2. Characterization of Historical and Projected Future Conditions

26

Figure 8.—Water rights closures in the Missouri Headwaters Basin study area.
Missouri Headwaters Basin Study

27

2.2. Future Challenges and Considerations

Changes in either water supply or demand can have a significant impact on 

communities, irrigators, hydropower plant owners, recreation interests, wildlife, 

and federally-listed species and their habitat. 

Water shortages are common and increasing in the study area overall (as 

summarized in the Impacts Assessment), and it is likely that the current 

imbalances between supply and demand will be intensified in the future due to the 

following factors: 

1) A warming climate and increased consumptive-use demands.

Reservoir storage decreases correspond with projected increases in 

agricultural demand and reservoir evaporation. Most scenarios indicate an 

increase in reservoir evaporation, coupled with decreases in precipitation 

for most scenarios. Reservoir evaporation may be offset by precipitation 

increases in other months. 

2) Changes in snowpack in headwater mountains with resulting changes 

in the amount and timing of snowpack runoff. The timing of inflow is 

projected to be earlier as one looks further into the future for most of the 

region’s reservoirs. Shifts in the volume and timing of snowpack storage 

will impact the region’s reservoir operations, particularly during spring 

when operations must balance competing objectives of flood control and 

water storage for irrigation deliveries later in the season. End-of-water 

year storage is projected to decrease in the future for most reservoirs 

modeled. 

3) Population growth and associated increased water demands.

Communities in the headwaters already face challenges in providing water 

for a growing population, such as the Gallatin Valley, because most of the 

flow in the basin has been appropriated for irrigation, hydropower, and 

municipal uses along with instream flows needed to support fisheries and 

recreation.

4) Other water demands. Water supplies for fish, wildlife, and recreation, 

and to conserve threatened and endangered species are also needed.

Future scenarios combined with paleohydrology show that future managed river 

conditions may be beyond the range of historical conditions and even conditions 

of the distant past, as suggested by comparisons between future scenarios and 

paleohydrology scenarios in the Impacts Assessment. Resource categories for four 

different regions within the study area are illustrated in Figure 9. Table 6

summarizes results from the Impacts Assessment for these categories.

Missouri Headwaters Basin Study

29

Figure 9.—Summary of Impacts Assessment results by region. 
2. Characterization of Historical and Projected Future Conditions

30

Table 6.—Summary of Impacts Assessment Results by Region within the Study Area

Rocky Mountain Front Upper Missouri Headwaters Musselshell and Judith River Basins Lower Missouri Mainstem

Water Deliveries

Centroid of 

streamflow 

timing

At least 35 days earlier for the 2050s and 

2080s.

5 to 15 days earlier on average by the 2080s for most future 

scenarios. 

15 to 25 days earlier on average by the 2080s. Generally smaller changes because flows are 

managed by upstream reservoirs. 

November—

March

Streamflow 

Increases with earlier peak. Increases for wetter scenarios and decreases for drier scenarios. Substantial increases for wetter scenarios and modest decreases 

or modest increases for drier. 

Modest increases for wetter scenarios and 

modest decreases or modest increases for drier

scenarios.

Snowpack Substantial decrease and much earlier date of 

peak snowpack.

Highest percent decrease in snowpack compared with other 

regions.

Modest decreases are anticipated. Mountainous areas that 

produce snowpack are relatively small.

Smaller decreases because region is primarily 

located plains where snowpack typically is low.

Water Demands

Agricultural 

Irrigation 

Demands

Increases are anticipated due to rising 

temperatures. Precipitation increases under 

most scenarios will not be sufficient to offset 

increasing demands.

Larger increases are anticipated than in other parts of the study 

area. 

Increases due to increasing temperatures, particularly Box Elder 

and Flatwillow sub-basins. 

Increases are anticipated with the Smith River 

basin increases projected to be more substantial 

increases. 

Reservoir 

Evaporation

Increases are generally anticipated, although 

increased precipitation for wetter scenarios 

could offset some evaporation increases.

Increases are generally anticipated, although for wetter scenarios 

increased precipitation could result in net evaporation decreases.

Increases are generally anticipated, although for wetter scenarios 

increased precipitation could result in net evaporation decreases.

Increases are generally anticipated, although for 

wetter scenarios increased precipitation could 

result in net evaporation decreases.

Reservoir Operations and Water 

Deliveries

Reservoir 

Storage

Greater inflow to Lake Elwell (Tiber Dam) for 

most months other than June through August; 

higher storage from January through June.

Higher or lower depending on the scenario at Canyon Ferry, Clark 

Canyon, Lima, and Ruby Reservoirs. Paleohydrology scenarios 

indicate a broader range of potential change than has occurred 

historically.

Higher or lower for Deadman’s Basin, Flatwillow, Bair, and 

Martinsdale Reservoirs, depending on the scenario. 

Paleohydrology scenarios indicate a broader range of potential 

change than has occurred historically.

Little effect on mainstem, run-of-the-river 

hydropower facilities. Higher or lower for North 

Fork of Smith, and Newlan Creek, depending on 

the scenario.

Deliveries 

and 

Shortages

Delivery shortages in the Sun River basin and 

in the Upper Marias River basin upstream are 

projected to increase because reservoirs will fill 

sooner, deliveries will begin earlier, and overall 

irrigation demands are expected to increase. 

Reservoirs are likely to fill and release stored water earlier in the 

year, leaving storage generally lower at the end of the season. 

Most headwaters irrigators with access to reservoir storage are 

expected to see increases in shortages. However, water shortages 

are projected to remain about the same or even decrease on 

average for Clark Canyon water users. 

Water shortages are projected to remain about the same or even 

decrease on average under wetter scenarios for reservoir users in 

the Musselshell and Judith River basins. Paleohydrology scenarios 

suggest that a greater range of reservoir inflows is possible than 

has occurred historically and much greater inflows are possible 

for some reservoirs, such as Flatwillow Reservoir. 

Scenarios suggest earlier filling of reservoirs due 

to streamflow timing changes and earlier 

drawdown to meet increased irrigation demands. 

Water shortages are projected to remain about 

the same or even decrease on average for those 

users of stored water in the mainstem Upper 

Missouri River and Smith River basins. 

Hydropower

Production Annual hydropower production is projected to 

decrease at Tiber Dam. Seasonally, decreases 

are projected for all months except for 

February through April, where the wetter 

future scenarios indicate a modest increase in 

production.

Average annual hydropower production at Canyon Ferry Dam may 

increase according to wetter future scenarios and decrease 

according to drier scenarios. Decreases are projected for most 

scenarios in July through December, while increases are projected 

for most scenarios in April and May. 

Reservoirs in the Musselshell River and Judith River basins do not 

have hydropower facilities. 

Future scenarios suggest greater annual 

hydropower production at NorthWestern Energy 

facilities for the wetter scenarios and reduced 

hydropower production for the drier. Production 

is expected to decrease under most scenarios 

during June through October and increase 

during January through April.
Missouri Headwaters Basin Study

31

Table 6.—Summary of Impacts Assessment Results by Region within the Study Area

Rocky Mountain Front Upper Missouri Headwaters Musselshell and Judith River Basins Lower Missouri Mainstem

Flood Control

Reservoir 

Storage in 

Flood Pool

Lake Elwell is projected to have more days on 

average in the flood pool. 

At Clark Canyon Reservoir, the average number of days above 

flood pool elevation may increase under wetter future scenarios 

and decrease in the near term under drier scenarios. At Canyon 

Ferry Reservoir, the average number of spring days per month 

above flood pool elevation is expected to increase, while the 

number of days during summer is projected to decrease. 

Further evaluation under the paleohydrology scenarios suggests 

that Clark Canyon and Canyon Ferry may go into the flood control 

pool more frequently in April through June and for longer periods 

of time (i.e., multiple years in a row). 

Reservoirs in the Musselshell River and Judith River basins do not 

have hydropower facilities, nor are they formally operated for flood 

control. 

Flooding will likely be an increasing challenge in the region 

because average annual runoff is generally projected to increase.

Hydropower reservoirs on the mainstem upper 

Missouri River and the smaller irrigation reservoirs 

in the Smith River basin are not formally operated 

for flood control.

Ecological Resources

Monthly

Streamflow

Summer flows are likely to increase under 

wetter future scenarios and decrease under 

drier future scenarios. Flows during winter 

months are likely to increase. Lower summer 

streamflow could further stress ecological 

systems. 

Summer flows are likely to decrease under most future scenarios 

and locations, except in the Beaverhead River basin where summer 

flows are largely projected to increase under most scenarios. Flows 

during winter months are likely to increase. Lower summer

streamflow could further stress ecological systems.

Mean monthly flows during spring and early summer months in 

the Judith River basin are likely to increase or decrease 

depending on the future scenario, while flows outside these 

months are projected to experience small changes. Mean 

monthly flows in the Musselshell River, on the other hand, are 

likely to increase for most months under future scenarios.

At Missouri River mainstem streamflow gage 

locations, flows are expected to increase during 

winter and spring months and decrease during 

summer and autumn months. High flows are 

projected to increase substantially by the 2050s 

and 2080s. Increases in high flows may provide 

benefits to ecological resources.

Ecological Resources (Continued)

7-day 

Average 

Maximum 

Streamflow

Likely to increase for the Sun River, Teton 

River, Marias River, and Dearborn River, 

particularly under wetter scenarios, and 

possibly decrease under drier scenarios. 

Increases in high flows may provide benefits to 

ecological resources.

Likely to increase for the Sun River, Teton River, Marias River, and 

Dearborn River for wetter future scenarios and even some of the 

drier future scenarios like at Red Rocks River. 

Projected to decrease under drier future scenarios and increase 

under wetter future scenarios in the Judith and upper Musselshell 

River basins. However, in the lower Musselshell River basin, all 

future scenarios indicate an increase.

For the Missouri River mainstem, high flows are 

expected to increase by almost twice as much by 

the 2050s and 2080s [check this]. For the Smith 

River, drier scenarios project decreases while 

wetter scenarios point towards increases. 

7-day 

Average 

Minimum 

Streamflow

Projected to decrease in the Dearborn River 

under most future scenarios but increase in 

the Marias and Teton basins. In the Sun River 

basin, future scenarios show decreases under 

drier scenarios and increases under wetter 

scenarios. 

May be higher under wetter scenarios or lower under drier future 

scenarios, except in the Beaverhead where increases are projected 

under most future scenarios. Theses minimums for some streams 

can occur during the winter and increases could be beneficial to 

ecological resources. 

For the Musselshell River basin, decreases are projected under 

drier future scenarios and increase under wetter future scenarios. 

In the lower Musselshell River basin, most future project an 

increase. Projected to decrease under most scenarios in the 

Judith River basin.

Drier future scenarios project decreases while 

wetter future scenarios indicate increases. For the 

Smith River, drier future scenarios indicate lower 

7-day average low flows, while wetter future 

scenarios indicate increases.

Recreation

Flatwater 

Recreation 

and River 

Floating

The future scenarios indicate a decrease in the 

average number of usable days at the boat 

ramps on Lake Elwell for all scenarios 

(assuming use is from April through October). 

This could result in reductions of overall 

recreational opportunities. 

At Clark Canyon (Beaverhead South, Lone Tree, and Horse Prairie 

boat ramps), more unusable days on average are projected for the 

future under all but the wetter future scenarios. At Canyon Ferry, 

there may be more unusable days overall under the wetter future 

scenarios and fewer unusable days under the drier future 

scenarios.

Boat ramp access for recreation has also not been quantified for 

reservoirs within this region. 

In the upper reach of the Smith River, between 

Sheep Creek and Eden, results indicate increases 

in higher flows from December - May and overall 

reductions during the remainder of the year. This 

could shift the popular recreational floating 

season on this stream to earlier in the year. Boat 

ramp access for recreation has not been 

quantified for reservoirs within this region

Missouri Headwaters Basin Study

33

3. Collaboration and Outreach

3.1. Background and Preliminary Outreach

Stakeholder outreach was a principal component of the Basin Study because it 

provided Montana DNRC and Reclamation the opportunity to explain current 

operational procedures and water management strategies in the study area and to 

engage stakeholders in planning for the future. Outreach for this Basin Study and 

the associated Impacts Assessment began in 2015 to inform stakeholders of study 

goals and objectives as well as to solicit input on technical aspects of the studies. 

This included future climate and runoff projections, construction of the Upper 

Missouri RiverWare planning model, and the identification of impacts measures.

In addition to fostering technical developments, this initial outreach helped the 

study team to establish contacts and informed Montana DNRC and Reclamation 

of the many ongoing related activities in the basin. For example, the collaboration 

on paleo-hydrology streamflow scenario aspects of the study with the USGS 

Northern Rocky Mountain Science Center was established during this initial 

outreach phase. 

Following this, other centralized meetings were held in Helena and Bozeman, 

with stakeholders from throughout the basin invited to attend. These meetings 

targeted agencies, researchers, non-governmental organizations (NGO) and 

watershed group coordinators. Other meetings were held in smaller communities. 

These were hosted by watershed groups or conservation districts to engage 

stakeholders who were knowledgeable and active in local water resource issues. 

Discussions at these meetings focused on study methods and results, identifying 

important issues, and developing strategies. 

Some of the key meetings and other stakeholders outreach activities are 

summarized in the following subsections. 

3.1.1. Upper Missouri Impacts Assessment Technical Meeting in 

Bozeman, Montana, July 9, 2015

This meeting primarily was attended by agency, university, and other water 

resources professionals to discuss and to solicit input on the technical aspects of 

the project. Participants were encouraged to present and discuss related activities 

that they were conducting in the basin. About 30 people attended the meeting. 

Key topics included: 

• West-wide Climate Risk Assessment

• Future scenario analysis for the Upper Missouri Basin Impacts 

Assessment

• Hydrology modeling, including model inputs and calibration 
3. Collaboration and Outreach

34

• Upper Missouri RiverWare planning model development 

• National Drought Resilience Partnership (NDRP) parallel efforts

• Metrics for evaluating potential water supply and demand impacts

3.1.2. Missouri Headwaters Impacts Assessment and Basin Study 

Workshop in Helena, Montana, December 1, 2016

About 35 people 

attended the meeting, 

and about another 10 

participated via the web 

and conference call. The 

attendees primarily were 

from agencies, 

universities, 

conservation districts, 

watershed groups, and 

non-profit organizations. 

During this meeting, the 

study partners presented 

preliminary future 

climate and runoff 

projections. 

Development and 

calibration of the Upper 

Missouri RiverWare 

planning model also was described. A discussion of future impacts on water 

supplies, demands and associated resources, and potential strategies followed. The 

participants also updated the group on their related activities in the basin. 

3.1.3. Upper Missouri Headwaters (UMH) Basin Task Force Meeting in 

Bozeman, November 8, 2017

Representatives of local watershed groups, non-profits, State and Federal 

agencies, the Montana State University system, the City of Bozeman, and drought 

coordinators for major watersheds in the Missouri Headwaters attended this 

meeting. Montana DNRC organized this meeting in conjunction with a 

WaterSMART program effort to produce a drought contingency plan for the 

Missouri Headwaters. The purpose was to share science and information on 

activities occurring in the Missouri Headwaters related to climate, water supply

and drought. A portion of the meeting agenda was devoted to discussing the Basin 

Study and Impacts Assessment, with emphasis on potential strategies. The 

remainder of the meeting was a facilitated group discussion by the Science for 

Nature and People Partnership (SNAPP) ecological drought working group team. 

This included small-group discussions on resilience and adaptation to drought in 

the Missouri Headwaters.

December 1, 2016, stakeholder meeting in Helena, Montana.
Missouri Headwaters Basin Study

35

3.2. Local Meetings

This outreach generally was conducted in conjunction with the regularly 

scheduled watershed group or conservation district meetings. Table 7 summarizes 

these meeting.

Table 7.—Local Meetings Attended during the Basin Study Process

Group Meeting Date Topics Presented and Discussed

Sun River Watershed 

Group (Great Falls)

11/12/2014 Study and analyses overview, timelines, and 

opportunities for participation

06/28/2016 Conference call to discuss operational 

procedures for Upper Missouri RiverWare 

planning model development

09/14/2016 Study progress report, discussion of Upper 

Missouri RiverWare planning model calibration, 

integration with group’s 10-year planning 

process

03/20/2017 Presentation of Impacts Assessment results, 

discussion of issues and strategies

Musselshell Watershed 

Coalition (Roundup)

06/13/2017 Presentation of Impacts Assessment results and 

preliminary modeling of strategies and 

discussion of issues

04/10/2018 Discussion of proposed off-stream storage 

strategy results

Beaverhead Watershed 

Committee (Dillon)

09/20/2017 Presentation of Impacts Assessment results, and 

identification and preliminary modeling of 

strategies and discussion of issues

Ruby Watershed Council

(Sheridan)

01/17/2018 Presentation of Impacts Assessment results, 

adaptation for anticipated future drought 

conditions, 2017 water budget, and potential 

future equivalents

Liberty County 

Conservation District

(Chester)

01/18/2018 Presentation of Impacts Assessment results with 

focus on Marias River basin, Lake Elwell

operations and modeling, potential strategies, 

and water for the Blackfeet Compact. 

The Blackfeet Tribe was contacted by the study team to identify possible needs 

for strategies related to tribal water rights and use. Although no strategies were 

identified to meet specific needs of the Blackfeet Tribe, one identified strategy 

does explore additional water use from Lake Elwell in the Marias River basin 

(Section 6.5.1: Providing Water for Future Consumptive Uses Through 

Canyon Ferry Reservoir and Lake Elwell).
3. Collaboration and Outreach

36

3.3. NDRP Montana Pilot Project

Partly due to the working efforts established for the Basin Study and Impacts 

Assessment, the Missouri Headwaters in southwest Montana was selected as one 

of two NDRP pilot projects, a collaboration of Federal and State agencies, NGOs, 

and watershed stakeholders. Several of the same Reclamation and Montana 

DNRC staff participated in this Drought Resilience project and Impacts 

Assessment/Basin Study, and many of the same stakeholders contributed to both 

processes. NDRP participants were interested in how the Impacts Assessment and 

Basin Study could inform future drought planning. Montana DNRC received 

Reclamation funding in 2018 through the WaterSMART program to produce a 

drought contingency plan for the Missouri Headwaters upstream of Canyon Ferry 

Dam which is in progress. This includes developing individual drought resilience 

plans for nine Missouri Headwaters tributary watersheds, and then incorporating 

these into a regional plan. Key meetings which Reclamation and Montana DNRC 

staff participated in included: 

• November 13 and 14, 2014 NDRP kick-off meeting in Bozeman

• March 17-18, 2015 workshop in Bozeman 

• September 9-11, 2015 work plan development meeting in Dillon

• May 23, 2018 drought contingency planning meeting in Helena 

3.4. Meetings with Other Entities

Informal meetings were held with other entities to gather information for the 

technical aspects of the studies and to solicit input on strategies. These meetings 

are summarized in Table 8. 

Table 8.—Informational Meetings Held with Other Entities

Group Meeting Date Topics Discussed

Montana DNRC State

Water Projects 

Bureau (Helena)

09/20/2017 Presentation of Impacts Assessment 

results with emphasis on State-owned 

dams and reservoirs, and potential use in 

upcoming Toston Dam Broadwater 

Hydropower Facility relicensing.

East Bench Irrigation 

District and local 

DFWP fisheries 

biologist (Dillon)

06/17/2016 Discussion of attributes to be considered in 

Upper Missouri RiverWare planning model, 

potential strategies, and fisheries 

considerations.

Helena Valley 

Irrigation District

(Helena Area)

07/19/2017 Background on Basin Study, tour of District 

facilities, and discussion of operations. 

Great Northern LCC

(Bozeman)

04/27/2017 Great Northern LCC activities and climate 

change at the large landscape level. 

Modeling and strategy considerations.
Missouri Headwaters Basin Study

37

3.5. Professional Meetings and Presentations

Presentations connected with the Impacts Assessment and Basin Study were given 

at professional meetings and conferences, including: 

Montana Section of the American Water Resources Association Conference, 

October 19, 2017, Helena, Montana: 

• Missouri Headwaters Impacts Assessment and Basin Study (Montana 

DNRC) 

• Applied paleohydrologic information for improved water management in 

the Upper Missouri River basin (USGS) 

Missouri River Natural Resources Council Conference, March 24, 2016, Great 

Falls Montana: Missouri Headwaters Basin Study: 

• Modeling future water supplies and demands, and operations of the basin 

upstream of Fort Peck Dam (Montana DNRC) 

University Council on Water Resources, Fort Collins Colorado June 13-15, 2017: 

• Upper Missouri Basin Impacts Assessment and Missouri Headwaters 

Basin Study (Reclamation)

2017 UCOWR/NIWR Annual Conference “Water in a Changing Environment”, 

June 14, 2017, Colorado State University, Fort Collins, Colorado: 

• Applied paleohydrologic information for improved water management in 

the Upper Missouri River basin (Montana State University) 

• Upper Missouri River Basin Impacts Assessment and Missouri 

Headwaters Basin Study (Reclamation)

3.6. Learning and Collaboration Opportunities

The outreach and collaboration process provided Reclamation and Montana 

DNRC an opportunity to inform the public, listen to their thoughts and concerns, 

and to learn about all the other interrelated activities in the study area. This was 

the first occasion for some people to learn about projected future water supplies 

and demands in a quantitative way. While the study partners found much interest 

in projections of future water supplies and demands, there also was some 

apprehension concerning our ability to meet future needs while maintaining

existing resource values. Representatives of agencies, universities, and non-profit 

groups that attended the meetings were interested in all the overlapping projects 

and eager to coordinate corresponding work efforts. The study partners also found 

a strong foundation for collaboration in the basin, especially through the 

established network of watershed groups and conservation districts. 

It was apparent from the collaboration and outreach process that changes to future 

operations and management will be constrained by existing contracts, 

commitments, and water rights considerations. On the other hand, it was evident 

that the stakeholders are willing to work together where they can to manage the 

system in a way that shares benefits across resources. 

Missouri Headwaters Basin Study

39

4. Interrelated Activities

4.1. Montana State Water Plan

The 2015 Montana State Water Plan (State Water Plan) set out a progressive 

program for the conservation, development, use, and sustainability of Montana’s 

water resources. In the State Water Plan, it was recommended that Montana 

DNRC: 

“work with local water users and other government agencies to 

conduct a basin-wide physical water availability and water 

management assessment in the Upper Missouri Basin. The study 

will assess and analyze how the basin’s existing water and power 

operations and infrastructure will perform under different water 

supply scenarios. The study will also analyze the effectiveness of 

adaptation and mitigation strategies for meeting the challenges of 

supplying adequate water in the future.” 

The Basin Study closely aligns with this objective of the State Water Plan 

recommendation. The Basin Study and the resulting Upper Missouri RiverWare 

planning model will be used by Montana DNRC as a planning and educational 

tool to help guide State Water Plan responsibilities under §85-1-203 MCA. In 

addition, Montana DNRC has other collaborative efforts in the Missouri 

Headwaters area with objectives that overlap with those of this Basin Study. 

4.2. The Montana Climate Assessment

The Montana Climate Assessment is an effort to synthesize, evaluate, and share 

credible and relevant scientific information about climate change in Montana with 

the citizens of the State (Whitlock et al. 2017). It is an assessment on climate 

trends and their potential consequences on Montana’s water, forests and 

agriculture. The Montana Climate Assessment is intended to be a sustained effort, 

with plans to regularly incorporate new information to address the needs of 

Montana. 

Because the Montana Climate Assessment was compiled during the same time as 

the Impacts Assessment and early phase of the Basin Study, there was some 

dialogue and overlap between the two efforts. For instance, hydrologic projections 

for the Montana Climate Assessment were developed using the Variable 

Infiltration Capacity (VIC) hydrology model web-based application, of which 

Reclamation was one of the developers. During a Musselshell Watershed 

Coalition meeting on June 13, 2017, which the Basin Study team presented at, the 

Montana Climate Assessment was also presented. The Montana Climate 
4. Interrelated Activities

40

Assessment report likewise contained a short description of the Basin Study. To 

validate some of the Impacts Assessment results, Reclamation compared them 

with the corresponding results from the Montana Climate Assessment. 

4.3. City of Bozeman Integrated Water Resources Plan

The City of Bozeman is growing and recognizes that its available water supply 

could be surpassed in the future as the population and water demands increase. 

Also, the city is in a basin that is closed to many types of new appropriations. The 

city also is concerned about the susceptibility of its water supply to drought and 

climate change.

In response to these concerns, the City of Bozeman has completed a detailed

Integrated Water Resources Plan (IWRP) to address water supply requirements 

over the next 30 to 50 years (Advanced Engineering and Environmental Services 

[AEES] 2013). The study estimates that its water supply/demand imbalance gap 

might range from 6,842 acre-feet to 17,752 acre-feet by the year 2062. These 

estimates were adjusted for projected climate change impacts on the water supply. 

In the IWRP, the City identified and evaluated various alternatives and alternative 

portfolios for meeting the additional projected future water needs. These included: 

implementing water conservation measures, adding water storage capacity, 

developing groundwater, purchasing senior water rights and water storage 

contracts, optimizing the capacity of existing sources, and developing non-potable 

sources for outdoor irrigation. 

4.4. Drought Planning

4.4.1. National Drought Resilience Partnership

The NDRP is a collaborative effort by Federal and State agencies, watershed 

stakeholders, and NGOs working to leverage and deliver technical, human, and 

financial resources to help address drought in the arid West. 

NDRP selected the Missouri Headwaters upstream of Canyon Ferry Dam in 

southwest Montana as one of two national drought resilience pilot projects. The 

basin was selected because the basin experiences frequent drought and faces 

rapidly increasing population and resource and land use changes. The NDRP 

Missouri Headwaters pilot study built on the Federal and State partnerships 

established for the Impacts Assessment (Reclamation 2019a) and this Basin 

Study, but this effort focused more on building resiliency to drought at the local 

watershed level. 

One purpose of the NDRP was to link drought information (e.g., monitoring, 

forecasts, outlooks, and early warnings) to longer-term drought resilience 

strategies in critical sectors such as agriculture, municipal water systems, energy, 

recreation, tourism, and manufacturing. The pilot initiative focused on how 
Missouri Headwaters Basin Study

41

improved drought preparedness at the local, State, and Tribal levels could be 

achieved through enhanced coordination with Federal agency and resources. 

The partners worked collaboratively to engage and train community-based 

drought coordinators to lead planning, mitigation, and project implementation in 

eight watersheds in the Missouri Headwaters. A project goal was to produce a 

model for information sharing, efficient water use, and community collaboration. 

It also prepared people to mitigate for drought while preserving cultural and 

ecological values in the face of a drier future. 

The project partners identified collective goals for developing community-based 

drought preparedness plans and long-term mitigation strategies to: 

1) Organize and engage watershed communities for local drought planning 

2) Provide tools for drought monitoring, assessing and forecasting 

3) Initiate local projects to build regional drought resiliency

4.4.2. WaterSMART Drought Contingency Planning

To build on the work of the NDRP Missouri Headwaters Project, Montana DNRC 

received Reclamation funding in 2018 through the WaterSMART Drought 

Program to produce a drought contingency plan for the Missouri Headwaters. The 

project is assisting communities with drought planning efforts with the support of 

local watershed drought coordinators and their Big Sky Watershed AmeriCorps 

members. These individual watershed planning efforts will provide the basis for a 

scaled-up, integrated regional Headwaters Basin Plan that considers watershed 

connections. These efforts are bringing together partners and resource agencies 

which have been collecting, analyzing, mapping, and sharing natural resource 

data in the Missouri Headwaters through the NDRP Montana Demonstration 

Project.

4.5. Water Compacts 

4.5.1. Blackfeet Tribe Compact 

The 2009 Montana Legislature passed a Compact settlement between the 

Blackfeet Tribe, the United States, and the State of Montana (§85-20-1501:1511, 

MCA). The Compact quantifies the reserved water right for the Blackfeet Tribe 

while protecting the rights of non-tribal water users locally and downstream on 

Birch Creek, Badger Creek, Cut Bank Creek, the Two Medicine River and the 

Milk River. The Compact was first introduced in Congress in 2010 and signed 

into law by President Obama on December 16, 2016. On April 20, 2017, 

Blackfeet Tribal members voted to approve the Compact. Interior Secretary Zinke 

executed the Compact on June 12, 2018. 
4. Interrelated Activities

42

The Compact encompasses streams in 

the upper Marias River basin, 

including the Birch Creek, the Two 

Medicine River, and Cut Bank Creek. 

In general terms, the Compact 

quantifies the water rights for the 

existing and future needs of the 

Blackfeet Tribe while minimizing 

impacts to the water supply available 

to other users. It specifies minimum 

flows for some streams. The Compact 

also provides a process for the Tribe 

to lease a portion of its water to offreservation users. There is a specific 

stipulation for the Birch Creek 

drainage which provides for 

coordinated management between 

Tribal and non-tribal users. Provisions for th

Blackfeet Indian Reservation.

e rehabilitation of the Four Horns 

Reservoir in the Badger Creek drainage would allow for water to be brought from 

there for use in the Birch Creek drainage. The Compact settlement also provides 

the Blackfeet Tribe an allocation to store water in Lake Elwell (Tiber Dam) of 

45,000 acre-feet per year which is available for the Tribe to use or market. 

4.5.2. Chippewa Cree Tribe-Montana Compact

This Compact covers the water rights of the Chippewa Cree Tribe of the Rocky 

Boy’s Reservation. Because the reservation mostly is within the Milk River basin, 

most of the Compact provisions apply to that drainage (§85-20-1001:1008, 

MCA). Pertinent to the study area, the Compact contains provisions to support 

Federal legislation that has passed and provides an allocation of 10,000 acre-feet 

per year of stored water from Lake Elwell (Tiber Dam) for any beneficial 

purpose, either on or off the reservation. 

4.5.3. Missouri Wild and Scenic River

This Compact between the State of Montana and the Bureau of Land Management 

(BLM) includes water for instream flow purposes in the Upper Missouri National 

Wild and Scenic River from Fort Benton to the Fred Robinson Bridge (§85-20-

501, MCA) and an instream flow stipulation for the Madison River within the 

Bear Trap Canyon Public Recreation site. The Compact provides for protection of 

all existing water rights under State law with a priority date before June 1, 2012, 

and for capped levels of new depletions (priority after December 31, 1987) in the 

Missouri River basin upstream, ranging from 35,000 acre-feet per month in 

October to 219,000 acre-feet per month during May. The stipulations for the Bear 

Trap Canyon Recreation Site provide a 1,100 cubic feet per second (cfs) yearround water right for the site with a June 9, 1971 priority date. 
Missouri Headwaters Basin Study

43

4.5.4. Upper Missouri River Breaks National Monument

This Compact was entered into by Montana and the United States to settle Federal 

reserved water rights claims for the Upper Missouri River Breaks National 

Monument, administered by the BLM (§85-20-1801, MCA). Relevant to the 

Basin Study are the minimum flows for the Judith River of 160 cfs, to be 

measured near the confluence with the Missouri River, and 5 cfs for lower Arrow 

Creek. The priority date for these rights is June 1, 2012. 

4.5.5. United States National Park Service

This Compact between the State of Montana and the U.S. National Park Service

covers five park units within Montana, three of which are in the Upper Missouri 

River basin study area, including Yellowstone National Park, the Big Hole 

National Battlefield, and Glacier National Park. The Compact generally provides 

surface water and groundwater for administrative purposes, instream flow, 

irrigation use, and emergency fire suppression (§85-20-401:402, MCA). Relevant 

to the study area are stipulations for instream flow water rights for the Big Hole 

National Battlefield, flows to Marias River tributary streams in Glacier National 

Park, and flows to Gallatin and Madison River tributary streams in Yellowstone 

National Park.

4.5.6. United States Fish and Wildlife Service

Compacts between the State of Montana and USFWS provide water in the study 

area for the Benton Lake National Wildlife Refuges as well as the Red Rock 

Lakes National Wildlife Refuge and Wilderness Area (§85-20-701, and §85-20-

801, MCA). In general terms, these Compacts allow for natural flow rights to fill 

refuge water bodies and for consumptive use, primarily by evaporation from 

water bodies and wetlands that provide wildlife habitat. Provisions are also 

included for the Red Rock Lakes Refuge for minimum flows in some streams and 

for the water needed to maintain lake levels. Administrative uses, such as wildfire 

suppression, also are protected. 

4.5.7. U.S. Forest Service

This Compact encompasses Federal reserved water rights for National Forest 

System Lands within the State of Montana and was approved in April 2007 

(§85-20-1401, MCA). This Compact recognizes reserved water rights for the 

U.S. Forest Service for administrative and emergency firefighting needs. The 

compact also uses Montana law to create state-based water rights for instream 

flow on the National Forest System lands, including those in the Missouri 

Headwaters. The Montana Water Court issued a final decree for this compact in 

October 2012. 

Missouri Headwaters Basin Study

45

5. Scenarios and Analysis 

Water resource managers across the Missouri Headwaters balance water supply 

and demand under complex rules and uncertain conditions. In long-term planning, 

managers must consider how investments made today could influence their ability 

to manage for both current and future challenges. Scenario planning offers 

multiple benefits for water resources planning, as it allows for the development of 

flexible, long-term plans and decision making where future conditions are 

uncertain. Development and analysis of scenarios are ways of systematically 

characterizing and combining different variables, events, conditions, or trends to 

reveal future problems or challenges and help to identify potential responses. The 

central purpose of scenario development is to understand the full range of 

possibilities for how future conditions may unfold. 

The Impacts Assessment and Basin Study use a scenario approach for quantifying 

water supply and demand, and for evaluating strategies. Scenarios of water supply 

include paleohydrology, historical conditions, and projected climate change 

(5 scenarios) under three planning horizons for the 21st century: 2020s, 2050s, and 

2080s (Figure 10). The approach, which is described in detail in the Impacts 

Assessment, uses a modeling framework to identify and evaluate possible water 

supply and demand imbalances under these different planning scenarios. Analysis 

includes: 

• Water supply under these scenarios was developed for surface water

through hydrologic and statistical modeling. Scenarios with additional 

groundwater pumping were modeled to deplete the surface water source 

based on aquifer characteristics.

• Water demands under these scenarios were developed by modeling 

evaporative demands from reservoirs and agricultural demands via 

evapotranspiration of crops. Demands also incorporate population 

estimates for municipal and industrial water use. 

• Management risk broadly refers to the potential failure of water 

resources infrastructure and management actions to meet water 

management objectives. Management risks under 2017 operating 

procedures were evaluated using the Upper Missouri RiverWare planning 

model, which incorporate inputs of water supply and demand to simulate 

river operations under various scenarios. 

Water supply and demand scenarios, as well as modeling for evaluation of water 

management risks, are discussed in following sections and detailed in the Impacts 

Assessment (Reclamation 2019a). Figure 10 provides an overview of developed 

scenarios of water supply and demand. These are described in more detail in the 

following sections. 
5. Scenarios and Analysis

46

Figure 10.—Components of the Missouri Headwaters Basin Study scenarios.

1

5.1. Water Supply Scenarios

Scenarios for evaluating possible water supply in the Upper Missouri River basin

in the future include historical conditions, paleohydrology, and future scenarios 

with and without paleohydrology. These scenarios are a key step in understanding 

future water supply within the study area and are summarized below and 

described in detail in the Impacts Assessment (Reclamation 2019a). 

Events that occurred in the distant past (paleohydrology) are included in the 

analysis because similar patterns of wet or dry years are likely to occur again.

With expertise from the USGS, this Basin Study makes use of paleohydrology 

(Martin and Pederson 2019), and more specifically extreme droughts (i.e., dry 

periods relative to the long-term average) and pluvial events (i.e., wet periods 

relative to the long-term average), to determine if there are conditions that 

occurred in the distant past that may affect the performance of strategies in ways 

the more recent historical period has not. 

The Basin Study uses paleohydrology in two ways: 

1) Extreme paleo events. Developing daily streamflow timeseries over 

50-year periods that encompass extreme drought and 50-year periods that 

encompass extreme pluvial events identified from tree rings (Most Intense 

Drought [MID], Most Intense Pluvial [MIP], Longest Drought [LD], and 

Longest Pluvial [LP]) 

1 WW: Warm wet future scenario; HW: Hot-wet future scenario; CT: Central tendency future 

scenario; WD: Warm-dry future scenario; and HD: Hot-dry future scenario.
Missouri Headwaters Basin Study

47

2) Future scenarios with paleohydrology. Identifying the same events 

combined with future streamflow scenarios (Warm wet [WW], Hot-wet 

[HW], Central tendency [CT] Warm-dry [WD], and Hot-dry [HD])

A relatively recent historical period (water years 1951 - 1999) simulation was 

used to provide a baseline for comparisons with paleohydrology and future 

scenario output. This simulation combines historical hydrology with current 

(2017) operational rules for river and reservoir management. The historical period 

(water years 1951 - 1999) was chosen due to the availability of stream gaging 

data, naturalized streamflow estimates, and hydrologic model data. This period, 

however, is bracketed by two intense historic droughts: the Dust Bowl drought of 

the 1930s - 1940s and the Millennium Drought between 2000 and 2010. The 

paleohydrology records were used to capture and test operation under extreme 

drought events such as these. 

Future scenarios were developed as a way of using the best available science for 

long-term planning under uncertain future conditions. The future scenarios 

provide our best estimate of what could occur over the coming century with 

respect to climate dynamics and warming. For this study, each scenario is 

considered an equally likely future planning scenario. These scenarios include 

five climate timeseries developed for the Missouri Headwaters that represent the 

range of projected changes in temperature (less warming to more warming) and 

precipitation (from decreases to increases):

• Warm-wet (WW):

Lower on the range of 

temperature change 

and higher on the 

range of precipitation 

change 

• Warm-dry (WD):

Lower on the range of 

temperature change 

and lower on the 

range of precipitation 

change 

• Central tendency 

(CT): Middle of the 

range of temperature 

change and middle of the range of precipitation change 

• Hot-wet (HW): Higher on the range of temperature change and higher on 

the range of precipitation change 

• Hot-dry (HD): Higher on the range of temperature change and lower on the 

range of precipitation change 

Badger Creek in the Marias River watershed headwaters.
5. Scenarios and Analysis

48

The climate timeseries are developed by adjusting historical climate over water 

years 1951 - 1999 to reflect projected changes from this baseline period to the 

2020s, 2050s, and 2080s future planning horizons. The resulting adjusted climate 

timeseries match the sequence of drought and pluvial events from the historical 

period and incorporate the effects of projected future climate. Each climate 

timeseries is then applied to models that simulate the effect of climate on 

hydrology in the region, including snow accumulation, snow melt, and surface 

runoff.

5.2. Water Demand Scenarios

Scenarios for evaluating water demand in the Missouri Headwaters include 

historical conditions and projected demographic and climate change. These 

scenarios are a key step in understanding future water demand and thereby the 

ability of future water supplies to meet this demand. The demands for water 

quantified for this Basin Study include: agricultural demands via crop 

evapotranspiration, evaporative losses from the region’s reservoirs, and M&I 

water use.

Water supply and demand scenarios were developed in parallel so that a water 

demand scenario corresponds to each water supply scenario. These scenarios are 

input to the Upper Missouri RiverWare planning model to evaluate conditions 

with or without strategies (described in Section 6). Water supply scenarios using 

paleohydrology were coupled with water demands over the more recent historical 

period (including agricultural demands, evaporative demands, and M&I 

demands). It was beyond the scope of this study to develop paleo-informed 

demands, which would require reconstruction of precipitation and temperature 

from the paleo record or substantial research into potential relationships between 

tree ring widths and historical plant water demand. 

The same recent historical period (water years 1951 - 1999) used for the historical 

water supply scenarios was also used to develop a baseline demand scenario for 

comparisons with paleohydrology and future scenario output. The recent 

historical period used as the baseline combines: modeled historical agricultural 

demands (assuming a crop mix from 2007 in the Upper Missouri River basin and 

2009 in the Musselshell River basin), modeled historical reservoir evaporation 

(assuming average reservoir depth), M&I demands for the largest municipalities 

(2017 estimates for Bozeman, Butte, Great Falls, and Helena), and current (2017) 

operational rules for river and reservoir management. 
Missouri Headwaters Basin Study

49

Future scenarios of water demand 

were developed by combining the 

same five future scenarios for water 

supply (WW, WD, CT, HW, and 

HD) with population projections for 

the largest municipalities for the 

2020s, 2050s, and 2080s. More 

specifically, future scenarios of 

agricultural demand incorporate 

future crop demands for water using 

the crop mix described above, future 

evaporative demands under a 

changing climate, and future M&I 

demands based on population 

growth. Because M&I demand is a 

relatively small fraction of overall 

demand in the region (about one 

percent), this study used a single future population growth scenario. 

As with other aspects of the Basin Study, there is uncertainty about future 

demand. The rates of regional economic growth, conservation efforts, shifting 

social preferences, and other factors that cannot be firmly predicted will affect 

future water demand in the Missouri Headwaters. As with the water supply 

scenarios, this approach evaluates a range of plausible future conditions regarding 

how—and how much—water will be used in the Missouri Headwaters into the 

future.

5.3. Upper Missouri RiverWare Planning Model

The Upper Missouri RiverWare 

planning model was developed as 

part of the Impacts Assessment to 

simulate current river and reservoir 

operations in the Upper Missouri 

River and Musselshell River and 

simulate water supply and demand 

scenarios, as well as strategies. The 

model was used to compute 

agricultural water deliveries, 

managed river flows, and reservoir 

levels throughout the study area, 

among other things. The model was 

developed using the RiverWareTM 

software (Zagona et al. 2001). 

Irrigation on the Greenfields Bench, Sun River. watershed.

Upper Missouri RiverWare Planning Model excerpt.
5. Scenarios and Analysis

50

Other basin studies have used RiverWare, including the St. Mary’s and Milk 

Rivers, Colorado River, Truckee River, and Klamath River Basin Studies. 

The historical scenario represents historical climate and hydrology alongside 

current operational and management conditions as of 2017. Various hydrologic 

and water demands scenarios previously discussed represent a range of plausible 

future conditions. These scenarios are examined within the current range of water 

development and management conditions to determine potential impacts of future 

changes through comparison with paleo-hydrologic scenarios and the historical 

baseline scenario.

5.4. Strategy Assessment Measures

In the Impacts Assessment and Basin Study, measures are used to evaluate and 

aid in the comparison of strategies for reduced imbalances in water supply and 

demand. These measures span numerous resource categories and were identified 

based on input from study partners, stakeholders, and resource managers in the 

basin. The measures presented in this study report and the reasoning behind using 

each measure are summarized in Table 9. 

Table 9.—Strategy Assessment Measures

Measure 

Category Measure Description Relevance 

Basin-wide 

Responses 

Change in the days of centroid of 

flow timing

Illustrates change in hydrologic regime

Change in end of month reservoir 

storage

Illustrates change in magnitude and 

timing of reservoir storage and 

effectiveness of operational policies

Change in annual reservoir inflow 

volume

Illustrates change in overall water supply

Change in April - October 

reservoir inflow volume

Illustrates change in hydrologic regime

Change in November - March 

reservoir inflow volume

Illustrates change in hydrologic regime

Water 

Deliveries

Change in end of water year 

reservoir storage

Illustrates ability of reservoir to meet 

summer storage demands

Change in irrigation supply 

shortages

Illustrates impacts to water users

Hydroelectric 

Power 

Resources 

Change in annual hydropower 

production at State, Federal, and 

private facilities

Illustrates impacts to hydropower 

production

Flood Control 

Operations

Change in days per month 

exceeding reservoir flood pool 

(Canyon Ferry, Clark Canyon, and

Lake Elwell) 

Illustrates change in potential flood risk
Missouri Headwaters Basin Study

51

Table 9.—Strategy Assessment Measures

Measure 

Category Measure Description Relevance 

Ecological 

Resources* 

Change in monthly streamflow Illustrates change in hydrologic regime

Change in the annual maximum 

7-day streamflow

Illustrates change in high flows which 

help move sediment, provide bank and 

overbank storage, and help alleviate 

disease

Change in the annual minimum 

7-day streamflow

Illustrates change in low flows which may 

stress fish and wildlife

Change in streamflow percentiles 

(5th, median, 95th) 

Illustrates change in hydrologic regime

Recreation Change in median unusable days 

at boat ramps

Illustrates impacts to flatwater boating 

recreation

Ecological resources include fish and wildlife habitat; species listed as an endangered, threatened, 

or candidate species under the ESA; flow and water dependent ecological resiliency; and 

water quality.

Missouri Headwaters Basin Study

53

6. Strategies

Strategies were developed to address water resource challenges identified in the 

Impacts Assessment, to address current issues identified by study partners and 

through stakeholder outreach, and to examine the impact of increased water 

demand. Strategies include changes to current water management practices, 

changes to existing infrastructure, and development of new infrastructure. 

Simulating the system under existing operations and with the existing 

infrastructure for various alternatives provides a baseline scenario (typically 

termed no-action) to which strategies can be compared. 

6.1. Formulation of Strategies

Strategies were developed to address future water needs and to adjust future water 

infrastructure operations to changing hydrologic conditions. The strategies also 

address major issues identified by the project partners and various stakeholders. 

Where possible, strategies have been developed to be proactive rather than 

reactive. That is, they were developed to make the system more resilient to water 

supply changes rather than to react to discrete circumstances when they occur. 

Because most of the future water supply scenarios project increases in average 

annual runoff, strategies also were formulated to evaluate changes in operational 

strategies that might be possible with increases in seasonal streamflow. 

6.2. Objectives and Constraints

While strategies were primarily developed to address gaps in water supply and 

demand, some were formulated to address multiple objectives while others were 

single purpose. Strategies include management changes, different operations for 

existing infrastructure, and structural changes, such as new off-stream storage 

reservoirs. Although a strategies’ ability to address water supply imbalances was 

addressed, they were not evaluated for economic or financial feasibility. Because 

the Missouri Headwaters is such a large area, not all strategies would affect the 

entire basin. Many of the strategies included here are specific to the larger 

Missouri River tributaries. Strategies were developed to be within the framework 

of the prior appropriation doctrine and how it is implemented through Montana 

state law, recognizing that water rights changes or new permits might be needed 

to implement some of the strategies. 

6.3. Approach to Strategy Identification

Using Reclamation and Montana DNRC knowledge of managed water resources 

in the study area as a starting point for considering input from stakeholders, 

strategies were identified to address present and potential future water supply 
6. Strategies

54

challenges and investigate the effects of increased water use in the study area and 

its tributaries. 

Known existing water supply/demand 

imbalances were then evaluated for future water 

supply and demands scenarios. Future conditions 

also were evaluated to assess whether there were 

any new imbalances in supply and demands that 

needed to be addressed. This was done on the 

basin and sub-watershed scale with focus on 

watersheds within Reclamation projects, such as 

the Beaverhead River, Sun River, and Marias 

River basins. Stakeholder meetings also were 

held at the basin and watershed scales to identify 

and evaluate strategies. 

6.4. Approach to Strategy 

Analysis

The following sections describe and evaluate the strategies by category or 

watershed. The first category of strategy presented is “Providing Water for Future 

Uses.” The two strategies within this category were developed to address future 

growth in the study area and not to alleviate impacts of future conditions. 

Subsequent presented strategies were developed to address concerns for water 

supply reliability and needs of fish and wildlife. Table 10 and Figure 11 list the 

strategies that were evaluated and are discussed below. 

Strategies were grouped by watershed if the strategy was focused on a particular 

watershed, and by strategy intent if the strategy focused on addressing a particular 

vulnerability. For example, three strategies seeking to improve water deliveries in 

the Sun River basin were evaluated together, while strategies investigating the 

effect of increasing irrigation efficiencies to improve water deliveries and 

investigating targeted high flow releases for ecological purposes were evaluated 

separately. Sets of performance measures for each strategy or groups of strategies 

were identified and a set of overview figures present summary information using 

these measures.

In the analysis that follows, background and objectives for each strategy are 

presented, followed by the strategy analysis and discussion of performance and 

tradeoffs. For each strategy, figures and tables may be presented to highlight 

specific aspects or benefits of the strategy. For each strategy category listed 

above, an overview figure summarizes impacts on various resource measures 

(described in Section 5.4. Strategy Assessment) under future and paleohydrology 

scenarios, with key findings highlighted. The overview figure also summarizes 

the effects of implementing a strategy compared with the current condition. 

Finally, the overview figure summarizes the effects of implementing the strategy 

under future and paleohydrology scenarios.

Canyon Ferry Dam.
Missouri Headwaters Basin Study

55

Figure 11.—Overview of strategy locations.

Missouri Headwaters Basin Study

57

Table 9.—List of Evaluated Strategies

Category Strategy Description

Providing Water for Future Uses

1 Providing Water for Future Consumptive Use through Contract Water 

from Canyon Ferry Reservoir and Lake Elwell

2 Providing Water for Future Municipal, Domestic, and Industrial Use in the 

Gallatin Valley

Pumping Groundwater with Corresponding Aquifer Recharge

Canyon Ferry Water Supply Pipeline

System-wide Water Management Strategies

3 Increasing Canal and On-farm Irrigation Efficiencies

4 Providing Ecological Flow Releases from Canyon Ferry Reservoir and Lake 

Elwell 

5 Beaverhead River Basin Strategies

Decreasing drawdown for Flood Storage and Clark Canyon Reservoir

Capping Winter Releases from Clark Canyon Reservoir to 100 cfs

Decreasing Flood Storage and Capping Winter Releases

6 Sun River Basin Strategies

Increasing Willow Creek Feeder Canal Capacity

New Off-stream Storage for Sun River Water

Increasing Pishkun Supply Canal Capacity

New Off-stream Storage and Increasing Pishkun Supply Canal Capacity

7 Musselshell River Basin Strategies

New Off-stream Storage in Lower Musselshell Watershed

8 Water Management Strategy for Increased Drought Resilience

6.5. Providing Water for Future Uses

Increased demand for water in the future is a likely scenario for long term 

planning, including agricultural water demand and M&I demand. Two significant 

factors are considered for future demands. The first is increasing irrigated acreage 

in the Canyon Ferry Reservoir area and in the Marias River basin near Tiber Dam. 

The second is providing water for new M&I uses in the Gallatin Valley, which is 

the fastest growing region in Montana. 
6. Strategies

58

6.5.1. Providing Water for Future Consumptive Uses through Contract 

Water from Canyon Ferry Reservoir and Lake Elwell

6.5.1.1. Background

Population growth and economic development could increase future water 

demands in the Missouri Headwaters. Because the study area upstream of the 

Great Falls and Teton watersheds is closed to most new appropriations of water 

with state-based water rights, contracting Reclamation-stored water from Canyon 

Ferry Reservoir and Lake Elwell might provide one of the few opportunities 

available for new water development in the future. Contract water could be 

pumped directly from the reservoirs or diverted from the Missouri River or 

Marias River downstream dams, from which targeted contract releases could be 

made. With the ability to store and regulate flow into the reservoirs, providing 

stored water through contracts could be a way to minimize impacts to other 

resources, when compared to potential impacts from direct flow diversions with 

no storage. 

Current Canyon Ferry water service contracts total approximately 9,100-acre-feet. 

Analyses by Reclamation indicate that there is about an additional 291,000 acrefeet available in the Canyon Ferry Reservoir for contracting, based on historical

flow data (Reclamation 2008). Much of the new development associated with 

Canyon Ferry Reservoir was anticipated to occur upstream of the reservoir, and 

this is now unlikely given the basin closures and instream flow rights described in 

Sections 1 and 2. However, there is the potential to develop new irrigated lands 

adjacent to the reservoir and along the Missouri River downstream through 

Reclamation contracts. Reclamation recently received a proposal from a private 

entity to develop about 12,000 acres of new irrigation on uplands just to the east 

of Canyon Ferry Reservoir. For this study, contracting of 50,000 acre-feet to 

supply 16,667 acres of irrigation was selected as a more realistic future maximum.

One of the original purposes for constructing Tiber Dam and Lake Elwell was to 

provide water for irrigation. Earlier analyses by Reclamation indicate that there is 

about 236,000 acre-feet available for contracting in Lake Elwell (Reclamation 

2008). Current irrigation water service contracts for the project total 

approximately 13,841 acre-feet, indicating that much of the demand estimated 

when Tiber Dam was constructed did not come to fruition. In 2005, Montana 

DNRC and Reclamation assessed the economic potential of a proposal by local 

irrigation proponents to pump water directly out of Lake Elwell to 20,000 to 

40,000 acres of bench lands to the northeast of the reservoir near Chester 

(Aquoneering 2005). 

Stored water from these reservoirs also could be used to meet future municipal 

and domestic water needs. The Rocky Boy’s North Central Regional Water 

Project is under development and is critical to fulfilling reserved water rights with 

the Chippewa Cree Tribe of the Rocky Boy’s Reservation and would provide 

water to other communities and rural water users in north-central Montana. The 
Missouri Headwaters Basin Study

59

City of Helena already has a water service contract for Canyon Ferry Reservoir 

water. Water service contracts from Canyon Ferry Reservoir also might provide 

opportunities for other municipalities and rural water users, including areas 

upstream.

Releases from Reclamation reservoirs might also be used to offset some of the 

impacts associated with the eventual development of irrigated lands from statebased water rights. In 1992, the Montana Board of Natural Resources and 

Conservation issued an Order granting water reservations to Conservation 

Districts in the Upper Missouri River basin for developing irrigated land in the 

future. The water reservation process identified lands with the best potential to be 

developed in the future. Although 18,675 acre-feet was reserved for the future 

development in the Upper Missouri River basin, only about 2,000 acre-feet of this 

water has been developed, due to basin closures and economic factors. 

Objectives

The objectives of this strategy are to identify a realistic potential expansion of 

future consumptive water demands for the Missouri Headwaters during the 

planning period (to 2099) and to investigate the potential role of contract water 

from Canyon Ferry Reservoir and Lake Elwell in meeting these demands and in 

mitigating potential impacts to other resources. This analysis is a starting point in 

developing strategies for meeting future consumptive use demands while 

sustaining other important resources. The additional developments considered in 

this strategy are summarized in Table 11. Because demands for water are a 

function of many factors, these demands may not fully be realized in the future or 

could be exceeded. 

This scenario includes adding 109,203 irrigated acres to the estimated 1.1 million 

acres currently irrigated. It is possible that irrigated acreages in other parts of the 

basin, such as the Gallatin Valley, could decline due to residential development 

and thereby offset some of the increases. The municipal/domestic pipeline 

projects were modeled to serve an additional 238,330 people. 
6. Strategies

60

Table 10.—Future Developments Included in the Strategy

Potential Development Source Description

Irrigation by contract from 

Canyon Ferry Reservoir

Canyon Ferry 

Reservoir

This was modeled as pipe-to-sprinkler 

irrigation that would be pumped from the 

reservoir. The modeled maximum annual 

volume was 50,000 acre-feet to supply 

16,667 acres of irrigation.

Irrigation by contract from 

Lake Elwell

Lake Elwell This was modeled as pipe-to-sprinkler 

irrigation that would pumped from the 

reservoir. The modeled maximum annual 

volume was 200,000 acre-feet to supply 

85,400 acres of irrigation.

Irrigation for State-based 

water reservations

Missouri River in 

lower portion of 

study area

This is the modeled future expansion 

based on current rates of development. It 

would include an additional 4,523 acres of 

sprinkler irrigation by 2050, and 7,136 

acres by 2080. 

Gallatin Valley pipeline for 

municipal and domestic use

Canyon Ferry 

Reservoir

This would include the pipeline described 

in the Gallatin Valley strategies. The 

maximum volume diverted per year would 

be 20,900 acre-feet.

Rocky Boy’s North Central 

Regional Water Project

Lake Elwell This would provide water to the Rocky 

Boy’s Indian Reservation and other small 

communities and rural areas in NorthCentral Montana. Annual contract volumes 

would be 4,640 acre-feet by 2020 and 

increase to 8,870 acre-feet by 2050.

Performance and Trade-Offs

The new irrigation development and water for municipal and rural growth could 

provide economic benefits, although these potential benefits are not quantified in 

this study. On the other hand, potential increased withdrawals from the reservoirs 

and associated water depletions could impact fisheries and aquatic resources, 

hydropower production, and recreation. There also is the potential for reductions 

to downstream flows and associated fisheries and hydropower benefits. Figure 12

presents modeled changes to resource measures with and without the strategy by 

scenario. 
Missouri Headwaters Basin Study

61

Figure 12.—Resource benefit changes comparison chart for Providing Water for Future Consumptive Uses through Contract Water 

from Canyon Ferry Reservoir and Lake Elwell strategy (2050s futures).

Missouri Headwaters Basin Study

63

6.5.1.3.1. Figure Orientation

In Figure 12, the percent change in performance measures, shown in the large 

upper panels, under different future and paleoclimate scenarios, as well as with 

different strategies, are presented relative to the historical baseline—which uses 

historical climate conditions, existing system configuration, and existing system 

operating rules. These changes are shown on the figures both as colors—

increasingly dark red for negative changes, and increasingly dark green for 

positive changes—and arrows indicating the direction of change—an up arrow 

(△) for positive change and a down arrow (▽) for negative change. If changes, 

positive or negative, are less than five percent, they are shown as no change. If 

changes, positive or negative, exceed one hundred percent, they are shaded as 

plus or minus one hundred percent and marked with a dot (•). 

The left panel shows performance under future and paleoclimate scenarios 

without strategies (baseline). The HD, HW, CT, WD, and WW future scenarios 

are shown along with the MID, LDP, MIP, and LP paleoclimate scenarios. This 

suggests how climate alone will impact system performance and identifies 

vulnerabilities under a range of different scenarios. Including both the future and 

paleoclimate scenarios also shows how the range of projected future change 

compares to historical variability. The reader may explore in these figures: do the 

future scenarios stay within the range of the paleoclimate scenarios, or do they 

exceed it, and in what measures? 

The middle panel shows how different strategies affect the performance measures 

under historical conditions. The reader may explore in these figures: had the 

strategy been implemented under current conditions, what effect does it have? 

The third panel shows the effect of strategies under future and paleoclimate 

scenarios. The reader may explore in these figures: do the strategies have a 

noticeable effect on the vulnerabilities identified in the first panel, and are the 

effects of the strategies seen under historical conditions in the second panel still 

evident under a range of scenarios? 

6.5.1.3.2. Figure Discussion

Canyon Ferry Reservoir end of water year storage was modeled to be a bit lower 

under most scenarios, compared with the baseline no strategy, while Lake Elwell 

(Tiber) end of water year storage was modeled to be substantially lower across 

scenarios. 

Modest reductions to flow were simulated for the Missouri River below Canyon 

Ferry (USGS Missouri River below Holter Dam gauge) and in the lower river 

(USGS Missouri River at Virgelle gauge) due to the increased development. The 

Holter gauge is downstream of Canyon Ferry Reservoir and indicates modeled 

reductions due to the Canyon Ferry water developments. The Virgelle station is 

below the mouth of the Marias River and reflects the combined developments 

associated with both reservoirs. More substantial flow reductions were modeled 
6. Strategies

64

for the Marias River at Loma associated with the new modeled water 

developments from Lake Elwell. Because the Marias River is a much smaller 

river than the Missouri River and increases in consumptive use are larger, the 

modeled effects of the new development on other resources are more pronounced. 

Modeled hydropower production decreased some for Canyon Ferry and the 

NorthWestern facilities with the strategy. This likely is due to an increase in the 

amount of water depleted from the system. The model results showed more 

substantial reductions to hydropower production at Lake Elwell, where relative 

depletions are greater. 

6.5.2. Providing Water for Future Municipal, Domestic, and Industrial 

Uses in the Gallatin Valley

Background 

Rapid growth is occurring in the City of Bozeman and the surrounding Gallatin 

Valley, and additional water likely will be needed to supply the increases in 

demand. The Missouri Headwaters are closed to applications for new permits to 

appropriate water, with some exceptions for surface water use by municipalities 

and applications to store water during high spring flows (§85-2-343, MCA). 

Moreover, local and downstream senior irrigation, storage, and instream flow 

water rights would generally preclude surface water development for new uses 

without more storage or changing an existing use. Groundwater is physically 

available in most valley areas, but because almost all accessible groundwater is 

connected to surface water, high-capacity wells without mitigation plans generally 

are precluded, although smaller wells (less than 35 gallons per minute and 

10 acre-feet per year) are mostly exempt from permit requirements (§85-2-306, 

MCA). These same constraints generally pertain to other areas in the Missouri 

Headwaters where domestic and M&I demands are increasing, although presently 

to a lesser extent than in the Gallatin Valley. At the same time, groundwater 

dynamics in the valleys are changing as agricultural land is developed for 

residential use. Irrigation recharge to aquifers is an important component to the 

hydrology of the Gallatin Valley, and reducing irrigation will decrease aquifer 

recharge. 

Table 12 illustrates potential increases in water demands (including indoor and 

outdoor) for the City of Bozeman and the remainder of Gallatin County over the 

Basin Study planning period. These demand projections presume an increase in 

water use efficiency and corresponding decrease in per-capita water diversion

based on percentage decreases from AEES (2013: Table 27. Medium 

Conservation, High Growth Reductions). 
Missouri Headwaters Basin Study

65

Table 11.—Projected Increases in Populations and Demands for the City of Bozeman and 

Other Communities and Rural Users in Gallatin County, Montana

Demands 2010 2020 2050 2080

Bozeman population 37,280 49,900 89,714 120,921

Smaller communities and rural 

population

47,204 63,184 113,596 153,111

Per-capita daily water demand 

(gpcd)

165 135 116 116

Annual demand all users (acre-feet) 15,615 17,100 26,417 35,607

gcpd = gallons per capita per day

In its integrated water resources plan (AEES 2013), the City of Bozeman has 

considered a number of options for meeting future water demands including: 

implementing water conservation measures, acquiring additional shares of Hyalite 

Reservoir storage, acquiring water rights with older priority dates, optimizing 

water use from existing sources, using non-potable water for irrigation, 

developing storage on Sourdough Creek, developing groundwater, aquifer 

recharge and recovery, importing water from the Yellowstone River basin, and 

importing water from Canyon Ferry Reservoir. However, Bozeman only accounts 

for less than half of the existing and projected population of the greater Gallatin 

Valley area. Future residents outside of the City of Bozeman generally will 

depend more on groundwater and may not have alternative water supplies such as 

the additional storage being considered by the City of Bozeman. 

Objectives

The objectives are to explore strategies that provide potential sources of water for 

future domestic and M&I demands in the City of Bozeman and the greater 

Gallatin Valley with a focus on those potentially linked to Reclamation’s Canyon 

Ferry project. Two options were evaluated for this strategy: 

1) High capacity groundwater wells in conjunction with aquifer recharge 

2) A conceptual pipeline from Canyon Ferry Reservoir to the Gallatin Valley 

For this Basin Study, the options are being examined in the context of the greater 

Gallatin Valley and include the future water needs for surrounding communities 

and unincorporated areas which have more limited water supply options. 
6. Strategies

66

6.5.2.3. Strategy 1: Pumping Groundwater with Corresponding Aquifer 

Recharge 

Under this strategy, high capacity wells drilled into Gallatin Valley aquifers 

would serve as the direct water source for increased domestic water demand.

Although groundwater use has advantages, such as resilience to seasonal shortage 

or drought and reduced treatment, withdrawals could affect existing water rights, 

including those for surface water. The source aquifer would be recharged with 

surface water during times of higher flow or through existing water rights 

purchases. These recharges could offset later depletions from the additional well 

pumping. 

The surface water diverted for aquifer recharge might be diverted from the 

Gallatin River, East Gallatin River, or tributaries and added to the aquifer through 

infrastructure such as existing irrigation canals, infiltration basins, injection wells, 

or green infrastructure (e.g., infiltration via permeable pavement). Aquifer 

recharge water might be secured from the following sources or from a 

combination of these sources: 

• Irrigation water rights: This potential source of mitigation water would 

be from purchasing, leasing, or changing irrigation surface water rights 

and then using the water to recharge the source aquifer storage rather than 

irrigating with it. Recharge water can be injected or infiltrated into the 

source aquifer through wells or engineered infiltration galleries or 

structures. Irrigation canals also are potential means for recharging 

aquifers or conveying water to aquifer recharge sites. Recharging with 

senior irrigation water rights would allow aquifer recharge to occur 

throughout the irrigation season, possibly providing greater ability to 

offset depletion to surface water during the winter and early spring. 

However, recharge with junior irrigation water rights might provide 

similar offsets with proper design of an aquifer recharge system and are 

more likely to be more available and less costly. 

• Canyon Ferry Reservoir water service contracts: During most years, all 

available flow from the Missouri Headwaters is captured, stored, and 

regulated by Reclamation at Canyon Ferry Dam. An upstream exchange of 

storable flow (where water would be stored in the aquifer rather than 

Canyon Ferry Reservoir) might be possible during times of high spring 

runoff by securing a contract for Canyon Ferry Reservoir water. As shown 

in Figure 13, during most years water is available for the Lower Gallatin 

River near Logan above senior Montana DFWP instream flow rights from 

April through early July. However, during the driest years, there is little, if 

any, water available above these rights. 
Missouri Headwaters Basin Study

67

Figure 13.—Normal range of streamflow for the lower Gallatin River near Logan 

compared to senior Montana DFWP instream flow rates. 

6.5.2.3.1. Performance

The model was used to evaluate the potential of using groundwater pumping in 

conjunction with aquifer recharge to: (1) supply water for future population 

growth in the greater Gallatin Valley, and (2) offset reductions to streamflow in 

the lower Gallatin River and Missouri River due to groundwater pumping. 

The rates of new demand were determined using projected per capita use rates 

and population growth. For the City of Bozeman, water would be pumped from 

groundwater wells if existing surface water supply is not sufficient to meet

demands. The rate and timing of depletions to surface waters was determined 

using the assumed efficiencies in the baseline model and lag factors consistent 

with the basin-wide return flow factors used for irrigation. Because the other 

Gallatin Valley users generally do not have access to alternative water supplies, 

future needs above and beyond use by the present-day population were all 

modeled to be met through groundwater. Due to distance from the source and well 

depth, pumping effects were modeled to result in constant year-round depletions, 

consistent with the assumed return flow patterns in the baseline. Depletions and 

the volume of water required for mitigation were assumed to be 52.5 percent of 

the pumped volume (Newfields and RESPEC 2017). The model results found that 

about 20,200 acre-feet would need to be pumped from groundwater annually to 

meet projected future needs by the 2050s. 
6. Strategies

68

Correspondingly, about 10,600 acre-feet per year of surface water on average 

would need to be recharged to groundwater to offset depletions. Aquifer recharge 

was modeled to occur through infiltration to the shallow aquifer at or near surface 

facilities for close to the annual volume depleted through aquifer pumping. Water 

was not added in the spring until irrigation demands commence, assuming that 

initial crop growth is a reasonable indicator that the ground is thawed for 

infiltration operations. When using high spring flow for aquifer recharge, the 

availability of high spring flow water is checked at Logan against the Montana 

DFWP instream flow right. When high spring flow is not available above this 

flow right, irrigation water is used as the source. To meet the aquifer volume 

recharge goals, water rights for up about 11,000 acres of irrigated land might need 

to be acquired by the 2050s (assuming irrigation water requirement of 1 acre-foot 

per acre; a greater consumptive use per acre would require acquiring less 

acreage). Water from aquifer recharge was modeled to return to surface water 

with a similar time lag as that used in the Upper Missouri RiverWare planning 

model for groundwater return flow from Gallatin Valley irrigation. The return 

flow factors were based on generalized aquifer characteristics for the Gallatin 

Valley. 

Figure 14 graphs rates of: (1) aquifer recharge, (2) recharge returns to surface 

water, and (3) modeled depletions to surface water due to groundwater pumping 

for a sample two-year sequence for the City of Bozeman component of the 

strategy. Aquifer recharge was generally modeled to start in April and continue 

through the late summer. Modeled returns of this recharge water to surface water 

exceeded depletions until the early spring when recharge again commenced. On 

an annual volumetric basis, more water was added to the aquifer than was needed 

to offset depletions due to pumping in the model, mostly because modeled 

percentages of the water pumped from groundwater consumed were less than 

initial expectations. However, as seen in Figure 14, this volume of mitigation 

might be required to ensure that winter flow depletions are fully covered. 

Additionally, some level of recharge above the depleted volume may be required 

to adequately mitigate any more local impacts to streamflow in individual 

streams, a level of analysis which has not been covered by this investigation. 
Missouri Headwaters Basin Study

69

Figure 14.—Modeled depletions to surface water compared to aquifer recharge rates and 

outflows from recharge to surface water. 

6.5.2.3.2. Other Considerations

6.5.2.3.2.1. Well Sites

Kendy and Bredehoeft (2006) investigated the effects of groundwater pumping 

and surface‐water‐irrigation returns on streamflow in the Gallatin Valley. They 

found that by strategically timing and locating artificial recharge within a basin, 

groundwater and surface water may be managed conjunctively to help maintain 

desirable streamflow conditions as land uses and irrigation practices change. They 

found that the most important factor in estimating stream depletion from pumping 

is the distance from the well to the stream and that artificial recharge near the 

pumping site is one way to achieve mitigation that conserves the quantity and 

timing of the stream depletion. 

Kendy and Bredehoeft (2006) used average aquifer characteristics for the Gallatin 

Valley. Moving aquifer recharge sites as far as possible from the surface water 

source would be one way to potentially further delay aquifer recharge returns. 

Artificial recharge could be sited most effectively to offset the effects of pumping 

if the aquifer materials are similar and the recharge site is the same distance from 

the stream as the pumping site. The shallow aquifer to 45 - 60 feet, where 

recharge might occur, is highly permeable while at depth, where water might be 
6. Strategies

70

pumped for M&I use, the aquifer materials become finer and it is less 

transmissive. Injection wells might be a way to add recharge water deeper in the 

aquifer and further attenuate returns to surface water. 

6.5.2.3.2.2. Institutional Framework 

During stakeholder outreach, questions were raised concerning whether the 

institutional framework exists to implement this type of strategy. Utility Solutions 

LLC, a privately held water and waste-water utility serving unincorporated areas 

near Four Corners in Gallatin County and recently purchased by Four Corners 

Water and Sewer District, has successfully mitigated new public water supply 

wells with existing junior irrigation water rights using an aquifer recharge basin 

(Montana DNRC 2015). 

Montana passed a state law in 2011 that allows existing water rights holders to 

change all or part of an appropriation for use as aquifer recharge or mitigation 

(§85-2-420, MCA). Part of the appropriation may be marketed (e.g., leased) or 

sold. A Gallatin Valley water exchange has been suggested as a way to facilitate 

water transactions for mitigating new groundwater use (Bren School of 

Environmental Science and Management 2016). Aquifer recharge mitigation with 

water rights and selling mitigation credits to new water users to offset effects of 

groundwater pumping was identified as a potential type of transaction a water 

exchange could facilitate. 

Given the physical and legal challenges associated with this strategy, aquifer 

recharge might be developed incrementally through multiple, dispersed recharge 

areas throughout the Greater Gallatin Valley, rather than as a single large facility. 

Mitigation facilities would likely be sited in areas of the valley where aquifer 

conditions and other factors are most conducive. 

6.5.2.3.2.3. Applicability

The strategy concept has been developed with the Gallatin Valley as a model, but 

it could be applicable to other Missouri Headwaters valleys to supply water for 

growing populations. Anticipated future changes to runoff timing would need to 

be considered in developing this strategy. This type of concept might be furthered 

developed and pursued by a city, NGO, or private entity. 

Strategy 2: Developing a Water Supply Pipeline from Canyon 

Ferry Reservoir Pipeline

This option models a 60-mile pipeline from Canyon Ferry Reservoir to deliver 

water upstream to the Greater Gallatin Valley. In its Integrated Water Resources 

Plan, the City of Bozeman considered a 36-inch diameter pipeline from Canyon 

Ferry Reservoir. The City also investigated the possibility of a shorter 30-mile 

pipeline which would divert water from the Missouri River upstream, near Three 

Forks. During the integrated water resources planning process, the technical 

advisory committee chartered by the Bozeman City Commission recommended 

against importing water from outside the Gallatin River basin due to costs, legal 

hurdles, and environmental concerns (AEES 2013). This would be a long-range 
Missouri Headwaters Basin Study

71

regional option, and it may only be practicable with support from the City of 

Bozeman and the other communities and rural water users in the Gallatin Valley, 

as well as possibly the State and Federal government. 

6.5.2.4.1. Performance

The model was used to evaluate pipeline water deliveries and potential impacts to 

other resources. Pipeline diversion demands were determined based on projected 

City of Bozeman and Gallatin Valley populations and per-capita use rates to 

follow the patterns shown in Figure 15. Modeled water demand from Canyon 

Ferry Reservoir for the City of Bozeman is that needed by the future population 

above what is modeled to supply the City under future climate scenarios from the 

City’s existing water sources. Other Gallatin Valley users were modeled to have 

their future water needs above historical be met solely with imported Canyon 

Ferry water. 

The pipeline was modeled to import about 20,200 acre-feet of water per year to 

the Gallatin Valley at an average rate of about 28 cfs. As with the previous 

strategy, the additional water would be diverted when existing water supplies 

were insufficient to meet demand. The rate ranged from a summer peak of up to 

about 58 cfs to a low in the winter of about 17.5 cfs (Figure 15). The water users 

outside of the City of Bozeman account for about half of the modeled diversions. 

Figure 15.—Modeled Canyon Ferry pipeline seasonal diversions for a sample two-year 

sequence.
6. Strategies

72

A consideration with importing Canyon Ferry water for municipal and domestic 

use is that it would need to be treated to remove arsenic to current water quality 

standards. This arsenic primarily originates from the Madison River headwaters in 

the geothermal areas of Yellowstone National Park. The City of Helena Missouri 

River Water Treatment Plant has been successful at treating Canyon Ferry 

Reservoir water to water quality standards (Helena Water Treatment Division 

2015). Water might be treated at the diversion site or elsewhere on the pipeline 

system.

A water service contract from Reclamation would be needed for this type of 

development. Water in Canyon Ferry Reservoir in the amounts need for this 

strategy was available for contracting under all future scenarios and extreme paleo 

event scenarios. The contract and features associated with the project, such as 

pumping facilities from the reservoir, would require a special use permit and 

compliance with the National Environmental Policy Act (NEPA) and National 

Historic Preservation Act (NHPA). Additional requirements typically associated 

with pipeline infrastructure (rights-of-way) would also need to be considered. 

6.5.2.4.2. Trade-Offs for Gallatin River Basin Strategies

Because these two strategies were developed to mitigate depletions to surface 

water, model results did not show appreciable changes to East Gallatin River and 

Lower Gallatin River streamflow (Figure 16). 

6.5.2.4.2.1. Figure Orientation 

In Figure 16, the percent change in performance measures, shown in the large 

upper panels, under different future and paleoclimate scenarios as well as with 

different strategies are presented relative to the historical baseline—which uses 

historical climate conditions, existing system configuration, and existing system 

operating rules. These changes are shown on the figures both as colors—

increasingly dark red for negative changes, and increasingly dark green for 

positive changes—and arrows indicating the direction of change—an up arrow 

(△) for positive change and a down arrow (▽) for negative change. If changes, 

positive or negative, are less than five percent, they are shown as no change. If 

changes, positive or negative, exceed one hundred percent, they are shaded as 

plus or minus one hundred percent and marked with a dot (•). 

The left panel in Figure 16 shows performance under future and paleoclimate 

scenarios without strategies (baseline). The HD, HW, CT, WD, and WW future 

scenarios are shown along with the MID, LDP, MIP, and LP paleoclimate 

scenarios. This suggests how climate alone will impact system performance and 

identifies vulnerabilities under a range of different scenarios. Including both the 

future and paleoclimate scenarios also shows how the range of projected future 

change compares to historical variability. The reader may explore in these figures: 

do the future scenarios stay within the range of the paleoclimate scenarios, or do 

they exceed it, and in what measures? 
Missouri Headwaters Basin Study

73

The middle panel shows how different strategies affect the performance measures 

under historical conditions. The reader may explore in these figures: had the 

strategy been implemented under current conditions, what effect does it have? 

The third panel shows the effect of strategies under future and paleoclimate 

scenarios. The reader may explore in these figures: do the strategies have a 

noticeable effect on the vulnerabilities identified in the first panel, and are the 

effects of the strategies seen under historical conditions in the second panel still 

evident under a range of scenarios? 

6.5.2.4.2.2. Figure Discussion 

An important consideration for Strategy 1: Pumping Groundwater with 

Corresponding Aquifer Recharge is that irrigated acres were reduced to supply the 

water needs for the municipal and rural domestic growth. This would substantially 

reduce irrigated acres in the Greater Gallatin Valley. 

Missouri Headwaters Basin Study

75

Figure 16.—Resource benefit changes comparison chart for the Providing Water for Future Municipal, Domestic, and Industrial Uses in the Gallatin 

Valley strategies (2050s futures).

Missouri Headwaters Basin Study

77

6.6. System-Wide Water Management Strategies

The strategies discussed in this section were developed as ways of alleviating 

current and possible future challenges related to water supply availability. There 

were two strategies identified that have implications for water supply and demand 

across much of the study area. These strategies include: 

1) Increasing on-farm and irrigation conveyance system efficiencies for all 

agricultural water users. 

2) Introducing ecological flow releases from Canyon Ferry and Tiber Dam. 

These strategies are further described in the sections that follow. Strategy 

performance and trade-offs were evaluated according to the assessment measures

discussed previously. 

6.6.1. Increasing Canal and On-farm Irrigation Efficiencies

Background 

There are about 1.1 million acres of land 

irrigated in the study area upstream of 

Fort Peck Reservoir. While much of this 

irrigation originated as gravity flood 

systems, the percentage of irrigation 

under center pivot and other sprinkler 

irrigation systems in Montana statewide 

increased between 1977 and 2008 from 

about 25 percent to about 45 percent

(Figure 17). Conversions to sprinkler 

irrigation are expected to continue, 

although there are limits to the 

conversion because not all lands are 

suitable for sprinkler irrigation. Changes 

also have been made to decrease losses 

from the delivery systems that convey water to the irrigated fields from the 

source, such as converting open ditches to pipelines and lining ditches. 

A flood irrigation system in the Ruby River valley.
6. Strategies

78

Figure 17.—Montana irrigation trends (source data: U.S. Department of Agriculture 

[USDA] undated).

Objectives

The objectives of this strategy are to 

investigate how trends towards 

increasing irrigation efficiencies might 

affect resources in the Missouri 

Headwaters (including the availability of 

water for irrigation and irrigation 

production, reservoir operations, 

hydropower production, recreation, and 

ecological resources) in the future and to 

investigate challenges and opportunities 

that this might create. Efficiency 

increases would include both on-farm 

and conveyance efficiencies. 

A sprinkler irrigation system in the Missouri River 

Valley near Townsend, Montana. 
Missouri Headwaters Basin Study

79

On-farm efficiencies: These conservation measures could include conversions 

from flood to sprinkler irrigation and more efficient flood irrigation water 

distribution, such as gated pipe, surge valves, land leveling, or shorter field runs. 

More efficient irrigation systems generally result in a larger percentage of the 

water applied on the field effectively meeting the crop’s evapotranspiration 

requirements.

Conveyance efficiency: These conservation measures involve the conveyance 

system—from the point of diversion on the stream or canal to the field. 

Efficiencies could include reducing losses to canal seepage and decreasing 

operational water spills off the end of the ditch system. Conveyance system 

improvements could include lining canals and laterals, putting lateral ditches into 

pipe, reducing operational spills by incorporating water measurement and 

automation into operations, reusing spills, and improving water management.

For this strategy, modeled irrigation efficiencies (combined on-farm and 

conveyance) were increased for each individual user group by 25 percent over the 

baseline (Reclamation 2019b), or to a minimum of 35 percent and maximum of 

72 percent. Table 13 summarizes the composite baseline efficiency and modeled

increased efficiency by major sub-basin. Sub-basins with large acreages operating 

with higher initial efficiencies or acres irrigated by groundwater would have 

percentage increases less than 25 percent. 

Performance and Trade-Offs for Increasing Canal and 

On-farm Irrigation Efficiencies

Although more efficient irrigation systems usually require less water to be 

diverted, more water generally will be depleted from the system through 

evapotranspiration, as irrigation water is delivered in a more uniform and timely 

manner. Table 14 compares irrigation depletion shortages for the Missouri 

Headwaters area above Three Forks, with and without the strategy. The 

reductions to depletions in the fourth column of the table correspond with the 

overall increase in the volume of water modeled to be depleted from the system. 

Table 12.—Modeled Increases in Irrigation Efficiencies Compared to Baseline by 

Sub-basin

Sub-basin Baseline Percent 

Efficiency

Strategy Percent 

Efficiency Percent Increase

Beaverhead 36.6 46.7 27.5

Big Hole 20.0 35.0 75.0

Boulder 26.0 35.0 34.6

Gallatin 39.6 49.2 24.3

Helena Valley 48.2 54.7 13.4

Jefferson 33.0 41.3 25.0
6. Strategies

80

Table 12.—Modeled Increases in Irrigation Efficiencies Compared to Baseline by 

Sub-basin

Sub-basin Baseline Percent 

Efficiency

Strategy Percent 

Efficiency Percent Increase

Judith 29.3 36.6 25.0

Madison 35.2 44.0 25.0

Upper Missouri 36.6 45.8 25.0

Marias 46.1 57.6 25.0

Missouri Below Great Falls 28.0 35.0 25.0

Upper Musselshell 22.2 35.0 57.7

Middle Musselshell 31.5 39.4 25.0

Lower Musselshell 35.3 44.1 25.0

Ruby 30.0 37.5 25.0

Smith 40.6 50.8 25.0

Sun 44.0 54.5 23.9

Upper Teton 56.0 70.0 25.0

Lower Teton 31.0 38.8 25.0

Area Weighted Average 36.2 46.8 29.3

Table 13.—Comparison of Irrigation Depletion Shortages for the Missouri Headwaters

Upstream of Three Forks under the Increasing Canal and On-Farm Irrigation Efficiencies 

Strategy

Scenario

Shortage 

without 

Strategy 

(acre-feet) 

Shortage with 

Strategy

 (acre-feet) 

Increased 

Depletions with 

Strategy (acrefeet) 

Change with 

Strategy (%)

Historical 202,957 154,961 47,996 23%

HD 2050s 363,341 293,699 69,642 19%

HW 2050s 275,857 211,470 64,387 23%

CT 2050s 311,547 246,061 65,486 21%

WW 2050s 213,121 160,093 53,028 25%

WD 2050s 282,260 223,040 59,220 21%
Missouri Headwaters Basin Study

81

6.6.1.3.1. Figure Orientation

Figure 18 summarizes modeled changes to resource measures at select locations 

due to the strategy for the period centered on the 2050s. In Figure 18, the percent 

change in performance measures, shown in the large upper panels, under different 

future and paleoclimate scenarios as well as with different strategies are presented 

relative to the historical baseline—which uses historical climate conditions, 

existing system configuration, and existing system operating rules. These changes 

are shown on the figures both as colors—increasingly dark red for negative 

changes, and increasingly dark green for positive changes—and arrows indicating 

the direction of change—an up arrow (△) for positive change and a down arrow 

(▽) for negative change. If changes, positive or negative, are less than five 

percent, they are shown as no change. If changes, positive or negative, exceed one 

hundred percent, they are shaded as plus or minus one hundred percent and 

marked with a dot (•). 

The left panel in Figure 18 shows performance under future and paleoclimate 

scenarios without strategies (baseline). The HD, HW, CT, WD, and WW future 

scenarios are shown along with the MID, LDP, MIP, and LP paleoclimate 

scenarios. This suggests how climate alone will impact system performance and 

identifies vulnerabilities under a range of different scenarios. Including both the 

future and paleoclimate scenarios also shows how the range of projected future 

change compares to historical variability. The reader may explore in these figures: 

do the future scenarios stay within the range of the paleoclimate scenarios, or do 

they exceed it, and in what measures? 

The middle panel shows how different strategies affect the performance measures 

under historical conditions. The reader may explore in these figures: had the 

strategy been implemented under current conditions, what effect does it have? 

The third panel shows the effect of strategies under future and paleoclimate 

scenarios. The reader may explore in these figures: do the strategies have a 

noticeable effect on the vulnerabilities identified in the first panel, and are the 

effects of the strategies seen under historical conditions in the second panel still 

evident under a range of scenarios? 

6.6.1.3.2. Figure Discussion

Irrigation shortages, as measured by the amount of water supplied to the crop 

relative to the demand, increase under future scenarios, but improved irrigation 

efficiencies lessen the impact, with shortage reductions being greatest under the 

HD and HW scenarios. There are some differences in the performance of the 

measure between watersheds. For instance, modeled decreases to irrigation 

depletion shortages in the Musselshell River basin are not as large as in the 

Rocky Mountain Front or Headwaters regions, possibly because the lengthy reach 

of this river allows irrigation returns from inefficient systems to continually be 

recycled and eventually depleted as water flows down the system. 

Missouri Headwaters Basin Study

83

Figure 18.—Resource benefit changes comparison chart for the Increasing Canal and On-farm Irrigation Efficiencies strategy (2050s futures). 

Missouri Headwaters Basin Study

85

For the Sun River in the Rocky Mountain Front, the water supply for most of the 

irrigated land is diverted in the upper portion of the Sun River basin and then is 

conveyed a considerable distance down the watershed by irrigation canals. It is 

not possible to re-capture most of irrigation returns because they flow into the 

very lower portion of the river, where there is a much smaller irrigated land base. 

Modeled shortage decreases were more pronounced here because of the limited 

opportunities to recycle water and because more efficient irrigation systems 

would consume more water overall. 

The results from a representative sample of river monitoring stations indicate that 

increasing irrigation efficiencies would generally decrease or not have a 

noticeable impact on average August streamflow (middle panel in Figure 18), due 

to a combination of modeled increases in the amount of water depleted and 

reductions to irrigation return flow. Streamflow reductions were modeled to be 

greater under the future climate scenarios (left panel). Reductions would be most 

notable in streams such as the Big Hole River, where baseline efficiencies are low 

and groundwater return flows, which contribute to late season flows would be 

reduced most. Lower late summer streamflow could have adverse effects on 

ecological resources and recreational opportunities. Overall, modeled percentage 

changes to August streamflow due to increased efficiencies were modest (right 

panel) because the efficiency increases were relatively small and because the 

hydrology model tends to overestimate late summer streamflow for most 

headwater streams.

The model results also indicate some modest reductions to hydropower 

production across future scenarios at Canyon Ferry Dam and the NorthWestern 

Energy facilities downstream. Increasing irrigation efficiency may result in 

slightly less average annual hydropower production under drier future scenarios. 

This likely is due to an overall increase in the amount of water depleted from the 

system and corresponding decrease in the flow of water through the turbines. 

Other Considerations

In some locations, it might be possible to achieve multiple resource objectives 

through irrigation efficiency improvements. For instance, in a highly regulated 

sub-basin, such as in the Sun River basin, as irrigation systems become more 

efficient there might be opportunities to mitigate potential late-season streamflow 

reductions through refinements to reservoir and delivery system operations. 

Linstead (2018) states that “A key first step should be to establish quantitatively

(e.g., using modelling and field observations) whether, in the specific context 

being considered, there is potential for increased irrigation efficiency to deliver 

ecologically relevant improvements to the timing of flows.” Evaluating these 

types of opportunities more specifically at the watershed scale would be a next 

step towards implementing this strategy. 
6. Strategies

86

6.6.2. Ecological Flow Releases from Canyon Ferry Reservoir and 

Lake Elwell

Background 

There is concern that flow regulation at Canyon Ferry Reservoir and Lake Elwell

have reduced the magnitude and frequency of downstream peak streamflow. 

Higher streamflow can mobilize streambed gravel and flush out accumulated 

sediment, which helps to provide an oxygen rich environment for fish eggs to 

incubate and provide habitat for aquatic insects which provide food for fish such 

as trout and whitefish. The Upper Missouri Watershed Alliance (UMOWA)

suggested that pulse flow releases from Canyon Ferry Reservoir, or periodic highflow events, would create a more natural state of the river and generally improve 

river health (UMOWA 2017). Further, these pulse flows might dislodge some of 

the excess aquatic vegetation on the streambed. UMOWA has begun a 

conversation with Reclamation, NorthWestern Energy, and the Montana DFWP

concerning the possibility of providing an annual large pulse flow to flush the 

Missouri River below Holter Dam. Ramping releases up to a peak of 14,000 cfs 

was suggested as a starting point. 

The Marias River immediately below Tiber Dam contains a trout fishery, and the 

river below the Highway 223 Bridge contains a variety of warm-water fish and 

serves as a spawning area for fish from the Missouri River. Tiber Dam (Lake 

Elwell) regulates the Marias River for flood control and for augmenting 

downstream flow when reservoir inflows are low. There has been interest in 

periodically releasing higher flows from Lake Elwell to mimic some of the predam variability of the natural flow regime downstream to benefit fisheries and 

riparian habitat. During 2006 when the reservoir was nearly full, Reclamation 

took the opportunity to make a pulse flow release from the reservoir, resulting in a 

June peak flow of about 4,800 cfs. An assessment after the release documented 

improved fisheries and riparian habitat (USGS 2008). Reclamation also made a 

pulse flow release for downstream fisheries, with a peak flow of about 4,000 cfs, 

during June 2014. 

Within the study area, the main stem of the Missouri River below the Great Falls 

and the Marias River represent the upstream extent of the Great Plains 

Management Unit (GPMU), one of four major management units identified in the 

2014 Pallid Sturgeon Revised ESA Recovery Plan. While the Great Falls of the

Missouri River are believed to have represented a natural boundary above which 

pallid sturgeon could not migrate, dams such as Fort Peck Dam on the Missouri 

River and Tiber Dam on the Marias River now present migratory barriers that did 

not exist historically. 

Additionally, the dams upstream of the Great Falls, including Canyon Ferry, 

affect river flow, temperature, and sediment and nutrient transport regimes which

are believed to affect the various life stages of pallid sturgeon. Within the Upper 

Missouri River basin, specifically, recovery strategies have focused on adaptive 
Missouri Headwaters Basin Study

87

management of reservoir flow releases, habitat protection, and restoration. 

Instream flow criteria specific to pallid sturgeon life history within important 

reaches of the Mainstem Missouri River and critical tributaries may be developed 

and implemented (USFWS 2014). 

Objectives

The objectives of this strategy are 

to evaluate the potential of 

ecological pulse flow releases 

from Canyon Ferry Reservoir and 

Tiber Dam to improve aquatic 

habitat in the Missouri and Marias 

Rivers, and potentially trigger 

pallid sturgeon spawning in the 

lower Missouri River. Modeled 

reservoir releases would begin 

with a lesser peak release in May 

to simulate prairie snowmelt and 

to initiate upstream movement in 

the lower Missouri River by 

native fish, including pallid 

sturgeon. This would be followed 

by a greater ramped-up reservoir release in June to mimic the mountain snowmelt 

hydrograph peak and to coincide with pallid sturgeon spawning. The flow would 

then be quickly ramped down to maximize pallid sturgeon larvae drift time 

following spawning (Figure 19). 

Modeled releases from each reservoir were simulated when the forecasted 

snowmelt season runoff volume exceeds the 20th percentile based on historical 

volumes. In years when the Canyon Ferry and Tiber Dams’ targeted flow releases 

were modeled to overlap, there would be more potential for benefits to ecological 

resources in the Missouri River downstream of the mouth of the Marias River due 

to the combined increase in flow. These benefits might include habitat and 

spawning conditions for the endangered pallid sturgeon, shovelnose sturgeon, 

paddle fish, sauger, and other warm-water species.

It is important to note that only streamflow in the Missouri River system above 

Fort Peck Reservoir was considered in modeling this strategy. During times of 

flooding, both locally and along the Missouri River in downstream states, flood 

control operations are coordinated by USACE, and releases such as those 

described under this strategy would not be made if they contributed to flood risks. 

Confluence of the Marias and Missouri Rivers near 

Loma, Montana. 
6. Strategies

88

Figure 19.—Example of Canyon Ferry and Tiber Dams coordinated release scenario.

Table 14.—Example Ecological Flow Release Scenarios Where Synchronized Releases were 

Modeled

Release 

Timing Reservoir Peak (cfs) Duration* (days)

Volume of Release 

(acre-feet)**

May and 

June

Canyon Ferry 15,000 50 462,039

Lake Elwell 5,000 50 207,025

Combined Release*** 20,000 50 669,064 *

This is the duration of the entire ecological flow releases, not just the peak.

**This is the volume of the release above the 4,000 cfs base release for Canyon Ferry Reservoir and 

the 500 cfs base release for Lake Elwell. ***This would not include additional tributary inflow that would occur downstream of the reservoirs.

Because most future scenarios predict increased runoff and inflow to Canyon 

Ferry Reservoir and Lake Elwell, this strategy might be able to take advantage of 

some of that inflow to make more frequent targeted releases to maintain 

downstream channel characteristics for fisheries and aquatic and riparian habitat 

and provide high flows for spawning fish. As shown in Table 15, a substantial 

volume of water would be required for these flow releases.
Missouri Headwaters Basin Study

89

Performance and Trade-Offs for the Ecological Flow Releases 

from Canyon Ferry Reservoir and Lake Elwell

Figure 20 depicts an example modeled release based on hydrologic conditions for 

the year 1956 when Canyon Ferry outflow was at the 15,000 cfs during the entire 

month of June and a release was made from Lake Elwell. The graph also shows 

how inflows from other tributaries, which were peaking at about the same time, 

contributed to boost the total flow at the Missouri River at the study area outlet at 

Landusky to over 30,000 cfs. 

Although the strategy did not appreciably increase the modeled highest peak flow 

rates for the lower Missouri River, it did demonstrate the potential to accomplish 

a couple of objectives: 

• First, it would allow for a controlled one-month release, which might be 

long enough to allow for native fish spawning. The relatively abrupt 

modeled drop in the flow at the time larval fish are emerging could 

increase the downstream drift time and might allow these larvae time to 

develop in the river where they are more likely to survive rather than 

getting swept into Fort Peck Reservoir. With a substantial inflow from the 

Marias River, some native fish might be impelled to ascend that stream 

during the time of the release, which could increase spawning habitat 

overall.

• Second, as the timing of spring runoff shifts earlier in the future, a 

managed release could be made that corresponds more closely with the 

long-established timing of fish migration and spawning. 

Projected future flow conditions might provide more opportunities for these types 

of ecological pulse flow releases. 

Figure 21 depicts the frequency for which these releases were modeled during a 

sample of 50-year periods which were developed with paleohydrology data to 

account for the range of flow conditions that occurred in the past and could occur 

again during the future. The black line overlaying each historical bar summarizes 

the number of qualifying releases made during the historical simulation period 

(water years 1951 - 1999). To further describe results shown in Figure 21 during a 

50-year period under historical conditions, targeted pulse flow releases were 

modeled to be made from Canyon Ferry reservoir from 1 to 12 years, from Tiber 

Dam in 5 to 16 years, and targeted releases from the two reservoirs were only 

modeled to overlap, at best, during only 1 of those year. For the HW future 

scenario, Canyon Ferry Dam releases were modeled to occur from 13 to 36 times 

during a 50-year period, Tiber Dam releases made ranged from 18 to 32, and 

releases overlapping releases were modeled to occur from 7 to 25 times. 
6. Strategies

90

Figure 20.—Example of a modeled ecological flow release based on 1956 conditions.

Figure 21.—Comparison of number of ecological flow releases for each reservoir and 

combined flow releases under historical and future scenario conditions.
Missouri Headwaters Basin Study

91

6.6.2.3.1. Figure Orientation

Figure 22 summarizes how ecological flow releases may impact other resources 

in the study area. In Figure 22, the percent change in performance measures, 

shown in the large upper panels, under different future and paleoclimate scenarios 

as well as with different strategies are presented relative to the historical 

baseline—which uses historical climate conditions, existing system configuration, 

and existing system operating rules. These changes are shown on the figures both 

as colors—increasingly dark red for negative changes, and increasingly dark 

green for positive changes—and arrows indicating the direction of change—an up 

arrow (△) for positive change and a down arrow (▽) for negative change. If 

changes, positive or negative, are less than five percent, they are shown as no 

change. If changes, positive or negative, exceed one hundred percent, they are 

shaded as plus or minus one hundred percent and marked with a dot (•). 

The left panel shows performance under future and paleoclimate scenarios 

without strategies (baseline). The HD, HW, CT, WD, and WW future scenarios 

are shown along with the MID, LDP, MIP, and LP paleoclimate scenarios. This 

suggests how climate alone will impact system performance and identifies 

vulnerabilities under a range of different scenarios. Including both the future and 

paleoclimate scenarios also shows how the range of projected future change 

compares to historical variability. The reader may explore in these figures: do the 

future scenarios stay within the range of the paleoclimate scenarios, or do they 

exceed it, and in what measures? 

The middle panel shows how different strategies affect the performance measures 

under historical conditions. The reader may explore in these figures: had the 

strategy been implemented under current conditions, what effect does it have? 

The third panel shows the effect of strategies under future and paleoclimate 

scenarios. The reader may explore in these figures: do the strategies have a 

noticeable effect on the vulnerabilities identified in the first panel, and are the 

effects of the strategies seen under historical conditions in the second panel still 

evident under a range of scenarios? 

6.6.2.3.2. Figure Discussion

The ecological flow releases were modeled to result in some decreases to late 

summer flow for the Marias River at Loma and to Lake Elwell’s end-of-wateryear (EOWY) storage (right panel in Figure 22 compared with left panel). 

Modeled hydropower production at Tiber did not change appreciably. Changes to 

other Canyon Ferry resources measures (e.g., hydropower production, reservoir 

levels, and streamflow at other times of the year) were modest but more than 

5 percent. These changes may be because the releases were limited to a maximum 

of 15,000 cfs due to downstream flooding concerns and were modeled to be made 

during wetter years, when similar releases would most likely be required under 

current reservoir operation procedures anyway. 

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Figure 22.—Resource benefit changes comparison chart for the Ecological Flow Releases from Canyon Ferry Reservoir and Lake Elwell strategy

(2050s futures). 

Missouri Headwaters Basin Study

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6.7. Beaverhead River Basin Strategies

Irrigation water shortages are 

common in the Beaverhead 

River basin and late summer 

streamflow in the Beaverhead

River between Clark Canyon 

Reservoir and the Barret’s 

Diversion Dam are projected to 

decrease under most future 

scenarios. This section 

investigates potential strategies 

for storing more water in Clark 

Canyon Reservoir to increase 

irrigation allocations during dry 

years and possibly improve 

Beaverhead River instream flow.

6.7.1. Decreasing the Drawdown for Clark Canyon Reservoir Flood 

Storage

Currently, 79,075 acre-feet of Clark Canyon Reservoir storage are allocated for

exclusive flood control. This upper zone of the reservoir only can be used to store 

water to reduce flooding downstream, and any water stored for flood control must 

be released promptly once the risk of flooding has passed. Under this strategy, 

20,000 acre-feet of this exclusive flood control zone would be reallocated to joint 

use where water could be stored for later release after the spring runoff peak has 

passed. The stored water would be released later to decrease irrigation water 

shortages and to improve summer flows in the 16 miles of the Beaverhead River 

between Clark Canyon Dam and the Barrett’s Diversion Dam for the East Bench 

Canal. 

6.7.2. Capping the Clark Canyon Reservoir Winter Release at 100 cfs

Minimum winter releases from Clark Canyon Reservoir are set by following 

guidelines based on the September 1 storage volume plus what the inflow volume 

was during July and August (Table 16). The maximum winter release of 200 cfs 

can result in a substantial reduction to the amount of water stored during the 

winter and it is thought that this could, in some cases, result in a reduced winter 

release rate during subsequent years. 

Clark Canyon Dam and Reservoir.
6. Strategies

96

Table 15.—Clark Canyon Winter Release Guidelines

September 1 Clark Canyon Reservoir storage plus 

July-August Inflow Volume (acre-feet)

Minimum Winter Release

(cfs)

Less than 80,000 25

80,000 - 130,000 50

130,000 - 160,000 100

160,000 or greater 200

This strategy’s objective is to provide a more consistent winter instream flow rate 

by reducing the maximum rate to 100 cfs during years when water supply 

conditions are wetter going into the winter. This might result in more carry-over 

storage for the instream flow during the following year and also reduce irrigation 

water shortages for the East Bench Irrigation District and Clark Canyon Water 

Supply Company users. 

6.7.3. Decreasing Flood Storage and Capping Winter Releases

This strategy would combine the decreased flood storage drawdown and winter 

instream flow release cap options described above. 

6.7.4. Performance and Trade-Offs for the Clark Canyon Reservoir 

Operational Strategies

The benefits from these strategies in reducing 

irrigation water shortages for the two water 

user groups that have contracts to Clark 

Canyon Reservoir Water, the East Bench 

Irrigation District and Clark Canyon Water 

Supply Company, might be subtle overall, but 

this strategy could provide important benefits 

during some drought years when water is at a 

premium. Figure 23 illustrates modeled results 

from the historical data set for a sequence of 

drought years in the late 1980s and early 

1990s. Modeled annual water allocations, as a 

percentage of full allocation, increased 

noticeably during drought years with the 

strategies, except during 1991 which was the worst drought year and near the 

middle of the sequence. For that year, the East Bench users were not modeled to 

have any water available to them, with or without the strategy. Because the plots 

in the graph for the capped winter release and combined strategies line up, it 

appears that most of the benefits would be attributable to the cap in the winter 

flow release from the reservoir. 

East Bench Irrigation District Canal.
Missouri Headwaters Basin Study

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Figure Orientation

Figure 24 shows changes to various resources by scenario associated with the 

three strategies discussed in this section. In Figure 24, the percent change in 

performance measures, shown in the large upper panels, under different future 

and paleoclimate scenarios as well as with different strategies are presented 

relative to the historical baseline—which uses historical climate conditions, 

existing system configuration, and existing system operating rules. These changes 

are shown on the figures both as colors—increasingly dark red for negative 

changes, and increasingly dark green for positive changes—and arrows indicating 

the direction of change—an up arrow (△) for positive change and a down arrow 

(▽) for negative change. If changes, positive or negative, are less than five 

percent, they are shown as no change. If changes, positive or negative, exceed one 

hundred percent, they are shaded as plus or minus one hundred percent and 

marked with a dot (•). 

The left panel shows performance under future and paleoclimate scenarios 

without strategies (baseline). The HD, HW, CT, WD, and WW future scenarios 

are shown along with the MID, LDP, MIP, and LP paleoclimate scenarios. This 

suggests how climate alone will impact system performance and identifies 

vulnerabilities under a range of different scenarios. Including both the future and 

paleoclimate scenarios also shows how the range of projected future change 

compares to historical variability. The reader may explore in these figures: do the 

future scenarios stay within the range of the paleoclimate scenarios, or do they 

exceed it, and in what measures? 

The middle panel of Figure 24 shows how different strategies affect the 

performance measures under historical conditions. The reader may explore in 

these figures: had the strategy been implemented under current conditions, what 

effect does it have?

The third panel shows the effect of strategies under future and paleoclimate 

scenarios. The reader may explore in these figures: do the strategies have a 

noticeable effect on the vulnerabilities identified in the first panel, and are the 

effects of the strategies seen under historical conditions in the second panel still 

evident under a range of scenarios? 
6. Strategies

98

Figure 23.—Modeled percent changes to Clark Canyon Water Supply Company and East 

Bench Irrigation District allocation fractions for a sample drought year sequence.
Missouri Headwaters Basin Study

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Figure 24.—Resource benefit changes comparison chart for the Beaverhead River basin strategies (2050s futures).

Missouri Headwaters Basin Study

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Figure Discussion

There would be some instream flow increases below Clark Canyon Dam during 

drought years in the river below Clark Canyon Dam associated with delivering 

water to the irrigation contract users (right panel compared with left panel). 

However, the opportunity for a winter instream flow release above 100 cfs during 

wetter years and associated benefits would be lost. Reservoir fisheries might 

benefit as model results showed higher end of water year reservoir levels for some 

scenarios. Under the increased flood pool and combined strategies, the time that 

the reservoir was in the exclusive flood control zone would notably increase. 

6.8. Sun River Basin Strategies

6.8.1. Background and Objectives

Water shortages are projected to increase for 

Sun River senior irrigation water users, 

including the Greenfields Irrigation District 

(GID), Fort Shaw Irrigation District (FSID), 

and Broken O Ranch. In particular, late 

summer streamflow for the Sun River at 

Simms is projected to decline under most 

scenarios. A system of canals and reservoirs 

provide water to Sun River irrigation users 

(Figure 25). Because the system is heavily 

regulated, operations are closely monitored 

through a series of stream and canal flow 

gaging stations to ensure that minimum streamflow is maintained and that flows 

for senior water rights and stored water are delivered to the intended users. 

These strategies investigate the potential for modifying some of the existing 

infrastructure associated with GID and FSID to reduce irrigation water shortages 

and improve the amount of time minimum instream flows are met and increase

reservoir storage levels. These strategies include managing water diversions and 

operations of the Willow Creek Reservoir, increasing the capacity of the Pishkun 

Supply Canal, and increasing off-stream storage available to GID. 

Sun River.

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Figure 25.—Map of the Sun River basin showing major hydrologic features, irrigation districts, and flow monitoring stations.

Missouri Headwaters Basin Study

105

6.8.2. Increasing Willow Creek Feeder Canal Capacity

This strategy’s objective is to investigate potential benefits to irrigation and other 

resources of increasing the effective capacity of the Willow Creek Feeder Canal 

(WCFC) from 75 to 175 cfs. The analysis was completed by using the Upper 

Missouri RiverWare planning model to model operations of the system with and 

without the canal capacity increase and compare resources benefits. 

Willow Creek Reservoir is an offstream storage reservoir for Sun 

River water. GID operates Willow 

Creek Reservoir to provide: 

1. Exchange water to 

downstream senior irrigators 

to offset GID diversions at the 

Sun River upstream at the Sun 

River Dam below Gibson 

Reservoir, primarily the FSID 

and Broken O Ranch senior 

users. 

2. Stored water to supplement 

the natural flow supply for FSID—about 

5,000 acre-feet of reservoir storage is allocated to FSID.

Willow Creek Reservoir holds about 31,848 acre-feet of water, with a usable 

capacity of about 30,000 acre-feet. The rest of the storage supports the reservoir 

fishery. The WCFC is the most important water source to the reservoir and has a 

design capacity of 500 cfs. The feeder canal receives water from the Sun River 

but discharges into a natural tributary to Willow Creek, where it flows for about 

10 miles before discharging into the reservoir. Substantial erosion has occurred in 

this natural channel and, as a result, recent operational procedures limit the 

maximum diversion down the feeder canal to about 75 cfs. The reservoir also 

receives some natural inflow from Willow Creek, which was included in the 

modeling analysis. Historical model runs, however, imply that the Willow Creek 

drainage might contribute about 7,500 acre-feet per year to the reservoir, on 

average. The maximum Willow Creek Reservoir outlet release, according to GID, 

is 350 cfs. 

Increasing the capacity of the WCFC generally would generally result in more 

water stored in the reservoir and a fuller reservoir at the end of the irrigation 

season. Figure 26 illustrates the impact of increasing the WCFC capacity to 

175 cfs under one of the HD paleohydrology scenarios for the 2080s future time 

horizon, which results in the lowest Willow Creek EOWY storage over a 50-year 

period. This sequence may be considered the worst-case scenario for Willow 

Creek storage. Although the increased feeder canal capacity would result in a 

Willow Creek Feeder Canal.
6. Strategies

106

typically fuller reservoir, note that during extreme drought years the reservoir 

would still be drawn down to minimum pool (2,233 acre-feet), with or without 

this strategy. 

Figure 26.—Modeled Willow Creek end of water year storage for the increased WCFC

capacity strategy for the worst case paleohydrology scenario compared to baseline 

conditions.

6.8.3. New Off-Stream Storage for Sun River Water

The objectives of this strategy are to assess the 

possibility and potential benefits of storing 

additional Sun River water off-stream. 

There is currently about 140,000 acre-feet of 

combined storage capacity in the three major Sun 

River Reclamation Reservoirs (Gibson, Willow 

Creek, and Pishkun). Although this is a substantial 

amount of storage, irrigation storage is mostly 

depleted by the end of August during many years. 

Increased storage might provide benefits to 

irrigation and other resources. During stakeholder 

outreach, GID envisioned that this new storage 

might be located on the main GID canal system, 

either on the Pishkun Supply Canal or upper portion 

of the Sunny Slope Canal downstream of Pishkun 

Reservoir. For future scenarios, peak reservoir inflows are projected to be earlier. 

For wetter scenarios, flows are projected to increase overall. If wetter conditions 

bear out in the future, this strategy might be a way to capture additional water for 

later release. 

Gibson Dam and Reservoir near the end 

of the irrigation season. 
Missouri Headwaters Basin Study

107

This strategy could include new reservoirs or expanding existing reservoirs. For 

this strategy, the new storage was modeled as located on main GID canal system 

through expansion of Pishkun Reservoir. An off-stream storage increase of 

 25,000 to 30,000 acre-feet was suggested by the GID manager. 

In simulating this strategy, the modeled maximum storage volume for the Pishkun 

Reservoir object was increased by 30,000 acre-feet—mimicking a new reservoir 

that would produce similar modeled results. 

6.8.4. Increasing Pishkun Supply Canal Capacity 

At times, diversions of water to storage in Pishkun Reservoir are constrained by 

the capacity of the Pishkun Supply Canal. With a higher canal capacity, it might 

be possible to convey more early-season Sun River water to off-stream storage. 

This could be advantageous in the future because most future climate scenarios 

are projecting increased early season flow. 

Under this strategy, the capacity of the Pishkun Reservoir supply canal would be 

increased from 1,400 cfs to 1,512 cfs (the reservoir outflow capacity) to 

potentially allow for the diversion of more water to the reservoir during peak 

flow times. 

6.8.5. New Off-Stream Storage with Increasing Pishkun Supply Canal

Capacity 

This strategy would combine Sun River Strategies 2 and 3. Modest reductions to 

irrigation shortages were modeled under the combined strategy, with most of the 

reduction due to the additional 30,000 acre-feet of off stream storage. This is 

demonstrated by Figure 27 which compares GID modeled baseline irrigation 

depletion shortages to those with the additional 30,000 acre-feet of off stream

storage, with and without an increase in the capacity of the Pishkun supply canal. 

Figure 27 illustrates the impact of these two strategies under one of the HD 

paleohydrology scenarios for the 2080s future time horizon, which results in the 

highest average GID shortages over a 50-year period. This sequence may be 

considered the worst-case scenario for GID. Modest reductions are in part due to 

the limited amount of additional water new off-stream storage could capture, 

which is explained further below. 

If new storage were to be constructed for use by GID, it is advantageous to 

evaluate how often the new storage would fill in a given scenario. The percentage 

of total new storage averaged over the simulation period was calculated under the 

historical scenario, 2050s future scenarios without paleohydrology, and extreme 

paleo event scenarios (MID, LDP, MIP, and LP) (Figure 28). Relative storage on 

July 1 was chosen because this is typically when the greatest volume of storage is 

available to GID, as July 1 is during the typical refilling period and the end of the 

runoff season. 
6. Strategies

108

Figure 27.—Modeled irrigation depletion shortages to GID considering additional offstream storage strategy and additional off-stream storage strategy with an increase in 

Pishkun Supply Canal capacity for the worst case paleohydrology scenario compared to 

baseline conditions.

Figure 28.—Modeled average percent full additional 30,000 acre-feet of off-stream 

storage would be with and without a modeled increase in capacity of the Pishkun Supply 

Canal, including historical and future 2050s scenarios as well as extreme paleo events.
Missouri Headwaters Basin Study

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In Figure 28, the new reservoir would not always be full on July 1. Further, under 

the historical scenario and most future scenarios, the new reservoir would be less 

than 50 percent full on July 1 on average. When modeled in conjunction with an 

increase in the capacity of the Pishkun Supply Canal, the additional storage was 

near about 10 to 20 percent fuller on July 1—meaning the new reservoir would be 

at least 50 percent full on average. Modeled July 1 storage was typically less 

under the future climate scenarios than the historical scenario, possibly due to 

irrigation demands beginning earlier in the year, with the additional modeled 

benefits of increasing the supply canal capacity to this measure being more 

distinct. 

6.8.6. Performance and Trade-Offs for the Sun River Basin Strategies

Figure 29 compares modeled changes in benefits provided by selected resource 

measures, with and without the strategies. 

Figure Orientation

In Figure 29, the percent change in performance measures, shown in the large 

upper panels, under different future and paleoclimate scenarios as well as with 

different strategies are presented relative to the historical baseline—which uses 

historical climate conditions, existing system configuration, and existing system 

operating rules. These changes are shown on the figures both as colors—

increasingly dark red for negative changes, and increasingly dark green for 

positive changes—and arrows indicating the direction of change—an up arrow 

(△) for positive change and a down arrow (▽) for negative change. If changes, 

positive or negative, are less than five percent, they are shown as no change. If 

changes, positive or negative, exceed one hundred percent, they are shaded as 

plus or minus one hundred percent and marked with a dot (•). 

The left panel shows performance under future and paleoclimate scenarios 

without strategies (baseline). The HD, HW, CT, WD, and WW future scenarios 

are shown along with the MID, LDP, MIP, and LP paleoclimate scenarios. This 

suggests how climate alone will impact system performance and identifies 

vulnerabilities under a range of different scenarios. Including both the future and 

paleoclimate scenarios also shows how the range of projected future change 

compares to historical variability. The reader may explore in these figures: do the 

future scenarios stay within the range of the paleoclimate scenarios, or do they 

exceed it, and in what measures? 

The middle panel shows how different strategies affect the performance measures 

under historical conditions. The reader may explore in these figures: had the 

strategy been implemented under current conditions, what effect does it have? 

The third panel shows the effect of strategies under future and paleoclimate 

scenarios. The reader may explore in these figures: do the strategies have a 
6. Strategies

110

noticeable effect on the vulnerabilities identified in the first panel, and are the 

effects of the strategies seen under historical conditions in the second panel still 

evident under a range of scenarios? 

Figure Discussion

Overall, changes in benefits were modeled to be modest with these strategies. 

Although irrigation water shortages are projected to increase substantially under 

most future climate scenarios, modeled decreases to water shortages were small 

for all strategies and under all scenarios. Increases in Willow Creek Reservoir 

EOWY storage were modeled for the increased Willow Creek Feeder Canal 

strategy under most scenarios. These increases in storage could result in increased 

reservoir recreational benefits. The strategies generally were not found to have 

substantial effects on the flow in the Sun River downstream. Gibson EOWY

storage could improve some under the combined additional off-stream storage and 

increased Pishkun Supply Canal strategies. This could be due to the increased 

storage and ability to divert higher flows into storage—resulting in less demand 

on Gibson Reservoir storage during some years. 
Missouri Headwaters Basin Study

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Figure 29.—Resource benefit changes comparison chart for the Sun River basin strategies (2050s futures).

Missouri Headwaters Basin Study

113

6.9. Musselshell River Basin Strategy

6.9.1. New Off-Stream Storage in the Lower Musselshell River Basin

Background 

In 2009, Montana DNRC received 

an application for a beneficial 

water use permit to construct a 

dam and reservoir in Horse Creek 

Coulee, a tributary drainage to the 

lower Musselshell River near 

Melstone. The reservoir’s primary 

purpose would be to provide 

supplemental water to irrigators 

on the lowermost Musselshell 

River who are subject to severe 

water shortages during drier years. 

This would be an off-stream 

storage reservoir for Musselshell River water. Flow would be diverted to the 

reservoir via the Southside Delphia-Melstone Canal. Some upgrades would need 

to be made to the canal to accommodate the new diversions. The reservoir would 

also capture some of the natural runoff from the Horse Creek watershed 

(30.2 square miles of drainage area). In Petroleum County Conservation District’s 

application for a water use permit (2009), the natural runoff was anticipated to be 

about enough water to offset reservoir evaporation and seepage. Releases from the 

reservoir would be used to supplement irrigation on the lower Musselshell River, 

and to enhance late summer instream flow in the lower river. Montana DNRC 

issued a water right permit for this project in 2011, but this project has yet to be 

constructed, primarily due to lack of funding. The Musselshell Water Users 

Association and Montana DNRC are considering funding alternatives. 

As described in the water permit applications, the project is anticipated to have a 

maximum storage capacity of 4,464 acre-feet and to supply about 1 acre-foot of 

supplemental water to about 2,500 acres of primarily flood irrigation along the 

Musselshell River downstream. The reservoir would be near the end of the 

Delphia-Melstone Canal, and improvements would need to be made to the canal 

to allow a desired diversion rate of 60 to 65 cfs to the new reservoir. As originally 

proposed, water would typically be stored in the reservoir during the spring and 

fall, with the specified diversion period being March 1 through November 15, and

with the reservoir releases from July 1 to July 31 at a rate of up to about 50 cfs. 

Potential benefits to streamflow are also identified, with a goal being the Montana 

DFWP target (water reservation) minimum flow of 70 cfs for the lower river. For 

recreational benefits, a minimum reservoir dead pool of 500 acre-feet is 

anticipated. 

Delphia-Melstone Canal description.
6. Strategies

114

Objectives

The objectives of this strategy are to evaluate the potential benefits of new offstream storage in the lower Musselshell River basin, using the Horse Creek 

Coulee Reservoir project as an example. Feasibility and sources of funding for 

executing this strategy were not considered in this analysis. The reservoir was 

modeled using the Upper Missouri RiverWare planning model. Water storage was 

modeled to occur during the fall and early spring and for releases for downstream 

irrigation at the rate needed to offset a shortage at any time during the irrigation 

season. During August and September, if stored water was still available, water 

could be released to supplement the instream flow in the lower river to bring the 

rate of flow closer to the Montana DFWP’s water reservation instream flow right 

of 70 cfs. Stored water was managed in the model to supplement the supply for 

2,500 irrigated acres, and a canal efficiency of 67 percent was assumed for 

deliveries to the reservoir. The canal that supplies the reservoir was assumed to be 

off from November 15 until March 1. 

Performance and Trade-Offs for the New Off-Stream Storage 

in the Lower Musselshell River Basin

The reservoir’s primary purpose would be to provide supplemental water to lower 

Musselshell River irrigators. Table 17 summarizes modeled reductions to 

irrigation shortages for lower Musselshell River irrigators. During wetter years, 

the reservoir benefits were smaller, because there typically is adequate direct flow 

water in the river to support the irrigation and little stored water needs to be 

released. During moderate flow years, this strategy would help provide water to 

fill the reservoir outside of the irrigation season and to meet a later demand for the 

stored water to reduce irrigation shortages. As the years become drier, however, it 

becomes difficult to fill the reservoir and consequently less water can be released, 

even though there is a substantial demand for stored water. For the driest 5 years, 

the strategy provides significant benefit only in the first year of an extended 

drought. 

Table 16.—Modeled Reductions to Irrigation Shortages Associated with the Horse Creek 

Coulee Reservoir using Historical Streamflow Data

Year Type

Decreases to Irrigation 

Diversion Shortages 

(acre-feet) 

Decreases to Irrigation 

Depletion Shortages 

(acre-feet)

Average for period 1,400 450

Wettest Ten Years 

(average)

477 134

Middle Ten Years 

(average)

2,226 782

Driest Ten Years 

(average)

1,095 324
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115

Year Type

Decreases to Irrigation 

Diversion Shortages 

(acre-feet) 

Decreases to Irrigation 

Depletion Shortages 

(acre-feet)

Driest 5 Years (average) 584 136

For this shortage-reduction assessment (Table 17), modeled conditions were 

based on historical streamflow data as input to the Musselshell River basin

portion of the Upper Missouri RiverWare planning model data. Streamflow data 

input to the model were based on historical streamflow data because of the 

uncertainties associated with the modeled streamflows, especially for the 

1,900-square mile Flatwillow Creek drainage, which enters the Musselshell River 

between the reservoir and the targeted irrigation. Flatwillow Creek is a flashy 

stream which is frequently dry during the summer. Based on gaging station data 

for the Musselshell River at Mosby, just below the Flatwillow Creek confluence, 

the hydrology model (VIC) appears to be overestimating contributions from 

Flatwillow Creek during the latter part of the irrigation season. Also for this 

analysis, the Upper Missouri RiverWare planning model was run for the period 

1950 - 2010 to capture the severe drought of the early 2000s. Local water users 

are mindful of the effects of that drought. 

Figure 30 depicts modeled storage for the reservoir for the 1950 - 2010 period. 

During about half of the years, the reservoir was filled to capacity and much or all 

of that stored water (to the minimum reservoir pool) was later released. Because 

both Martinsdale and Deadman’s Basin Reservoirs upstream have considerable 

off-stream storage capacity and senior water rights, the reservoir was not modeled 

to fill during dry years. Indeed, during extended drought, there may be sequences 

of years where the reservoir would be able to store little—if any—Musselshell 

River water. During the drought of the late 1980s and early 1990s, storage and 

releases were around 1,000 acre-feet per year or less. For the early 2000s, the 

simulations showed 5 years in a row where almost no water was modeled as being 

stored. There were a few years, generally dry years followed by wetter years, 

where nearly the full active storage capacity of the reservoir (about 4,000 acrefeet) was modeled as being released. 

As stated earlier, the proposed reservoir was also intended to provide some 

instream flow benefits during the latter part of the irrigation season. Thus, 

increases to flow at Mosby are generally projected for the July through September 

period, as water is released for supplemental irrigation downstream of this 

monitoring point. However, there are modeled reductions to flow during times 

when the reservoir is generally storing water, typically during the fall after the 

irrigation season and early spring. While reducing flows during these periods, the 

reservoir was simulated to only store water when flow at Mosby exceeded 

Montana DFWP’s 70 cfs instream flow right. 
6. Strategies

116

Figure 31 summarizes changes to resource benefits, for historical conditions 

relative to future scenarios and extreme paleo events, and with and without the 

reservoir. 

Figure 30.—Modeled Horse Creek Coulee Reservoir storage for 1950 - 2010 historical 

period.

6.9.1.3.1. Figure Orientation

In Figure 31, the percent change in performance measures, shown in the large 

upper panels, under different future and paleoclimate scenarios as well as with 

different strategies are presented relative to the historical baseline—which uses 

historical climate conditions, existing system configuration, and existing system 

operating rules. These changes are shown on the figures both as colors—

increasingly dark red for negative changes, and increasingly dark green for 

positive changes—and arrows indicating the direction of change—an up arrow 

(△) for positive change and a down arrow (▽) for negative change. If changes, 

positive or negative, are less than five percent, they are shown as no change. If 

changes, positive or negative, exceed one hundred percent, they are shaded as 

plus or minus one hundred percent and marked with a dot (•). 

The left panel shows performance under future and paleoclimate scenarios 

without strategies (baseline). The HD, HW, CT, WD, and WW future scenarios 

are shown along with the MID, LDP, MIP, and LP paleoclimate scenarios. This 

suggests how climate alone will impact system performance and identifies 

vulnerabilities under a range of different scenarios. Including both the future and 

paleoclimate scenarios also shows how the range of projected future change 

compares to historical variability. 
Missouri Headwaters Basin Study

117

Figure 31.—Resource benefit changes comparison chart for the Musselshell River basin strategy (2050s futures).

Missouri Headwaters Basin Study

119

The reader may explore in these figures: do the future scenarios stay within the 

range of the paleoclimate scenarios, or do they exceed it, and in what measures? 

The middle panel shows how different strategies affect the performance measures 

under historical conditions. The reader may explore in these figures: had the 

strategy been implemented under current conditions, what effect does it have?

The third panel shows the effect of strategies under future and paleoclimate 

scenarios. The reader may explore in these figures: do the strategies have a 

noticeable effect on the vulnerabilities identified in the first panel, and are the 

effects of the strategies seen under historical conditions in the second panel still 

evident under a range of scenarios? 

6.9.1.3.2. Figure Discussion

Irrigation shortages for lower Musselshell water users are modeled to increase 

substantially in the future, with and without the reservoir. The reservoir was 

modeled to reduce those shortages under historical conditions but not noticeably 

under the future scenarios. Small changes to streamflow for the lower Musselshell 

River at Mosby were modeled for the future scenarios. Compared to historical 

conditions, the average reservoir levels were modeled to be similar to historical 

under the wetter future scenarios, and lower than modeled historical for the drier 

scenarios. 

6.10. Water Management Strategy for Increased 

Drought Resilience

6.10.1. Background 

Drought has been a regular 

occurrence in the Missouri 

Headwaters in the past and will 

continue to be in the future. 

Historical droughts have 

significantly stressed agriculture, 

recreation, and fisheries and 

other ecological resources. Even 

during years when there is a nearaverage total water volume, late 

season water shortages can cause 

significant impacts, such as occurred during the late summer “flash” drought of 

2017. The worst drought in the historical record for most areas in the Missouri 

Headwaters was the Dust Bowl drought of the 1930 - 1940s. As severe as that 

drought was, the paleohydrology streamflow scenarios indicate that numerous 

droughts of similar or greater magnitude and duration have occurred in the more 

distant past (Figure 32), and the drought cycles of the future will be affected by 

changes in flow timing, precipitation, and temperatures. 

Monitoring streamflow on the Ruby River.
6. Strategies

120

Figure 32.—Droughts in the Missouri Headwaters during the last 1,200 years.

Although future climate projections for the Missouri Headwaters could be 

interpreted as tilting towards wetter conditions, due to increased average annual 

streamflow, the annual streamflow measure can be misleading. Summer and early 

fall streamflow, when water demands typically are highest, generally is projected 

to decrease in the Missouri Headwaters under future scenarios. In addition, 

demands are projected to increase and late summer precipitation, which when 

timely can lessen irrigation demands, generally is projected to decrease as well. 

The earlier snowmelt and lower late-season flow projected for the future, could 

lead to increase competition for water during the peak growing season in the 

future and add to drought vulnerability. 

During stakeholder outreach for the 2015 Montana State Water Plan, there was 

considerable discussion of drought and whether drought intensity, frequency, and 

duration might increase in the future. With the drought of the early 2000s still 

fresh in everyone’s minds, a paramount concern was how to maintain our waterbased resources and economy in the Missouri River Headwater through times of 

drought. 

At about that same time, there was a Federal initiative to demonstrate how 

communities could plan and prepare for drought, which led to the National 

Drought Resilience Partnership (NDRP) Pilot Program. The Missouri Headwaters 

Drought Resiliency Project was initiated in 2014 as part of this National pilot 

program to engage communities in the development and implementation of local 

watershed drought resilience plan through a collaborative effort by State and 

Federal agencies, watershed stakeholders, and NGOs. The pilot study was linked 

to the State and Federal partnerships established for the Impacts Assessment and 

Basin Study in the Upper Missouri Headwaters, but with efforts focused more at 

creating resiliency to drought in the face of a changing future at the local 

watershed level. 
Missouri Headwaters Basin Study

121

To further build on the work of the NDRP Missouri Headwaters Project, Montana 

DNRC received Reclamation funding in 2018 through the WaterSMART program 

to produce a drought contingency plan for the Missouri Headwaters upstream of 

Canyon Ferry Dam. This includes developing individual drought resilience plans 

for eight Missouri Headwaters tributaries watersheds and then incorporating these 

into a regional plan that considers downstream connections and evaluates drought 

resilience from a regional perspective. 

6.10.2. Objectives 

This strategy’s objectives are to continue ongoing efforts to build drought 

resilience capacity in the Missouri Headwaters to prepare to manage drought 

when it occurs as well as to incorporate and adapt to changing drought 

characteristics in the future. The strategy will continue the efforts begun through 

the NDRP and Reclamation drought contingency planning processes by preparing 

for drought rather than responding to crises as they occur. The partners will 

continue to work collaboratively to engage and train community-based drought 

coordinators to lead planning, mitigation, and project implementation in eight 

watersheds in the Missouri Headwaters. These ongoing efforts will prepare 

stakeholders to mitigate for drought while preserving cultural and ecological 

values in the face of a changing future. 

Specific tasks will include linking drought information (e.g., monitoring, 

forecasts, outlooks, and early warnings) to longer-term drought resilience 

strategies in critical sectors such as agriculture, municipal water systems, energy, 

recreation, and tourism. 

The project partners identified collective goals for developing community-based

drought preparedness plans and long-term mitigation strategies in the Missouri 

Headwaters: 

1) To organize and engage watershed communities for local drought 

planning 

2) To provide tools for drought monitoring, assessing, and forecasting 

3) To initiate local projects to build regional drought resiliency 

As part of the project, the Missouri Headwaters Task Force was formed to assist 

communities with local drought contingency planning efforts and to support local 

drought coordinators and their Big Sky Watershed AmeriCorps members. The 

individual watershed planning efforts will provide the basis for a scaled-up, 

integrated Headwaters Basin Plan. These efforts also are bringing together 

partners and resource agencies that have been collecting, analyzing, and mapping 

natural resource data in the Missouri Headwaters. This is a proactive approach to 

drought as envisioned in Reclamation’s WaterSMART Drought Response 

Program Framework, to implement actions to build long-term resiliency to 

drought. 
6. Strategies

122

Other aspects of this strategy would include: 

• Monitoring system: The drought monitoring network is being expanded 

through planning efforts to allow coordinators to better quantify water 

supplies and establish procedures to identify the onset and severity of 

drought. As an example, the coordinator in the Ruby River basin has 

developed a comprehensive tributary gaging project to monitor the 

contributions of flow to the Ruby River downstream of the Ruby 

Reservoir. Other participants in the original NDRP process are developing 

drought monitoring tools that will be used by the coordinators, such as the 

Montana Climate Office’s development of a statewide soil moisture and 

meteorological information system called the Montana Mesonet (Montana 

Climate Office 2018). 

• Vulnerability assessment: Assessing risk requires a review of past drought 

impacts, an analysis of historical water supply and water use trends, and 

projections to show how those trends may change over time. The results of 

the Impacts Assessment will be used in developing the vulnerability 

assessments, including the range of potential future drought conditions. 

• Mitigation and response actions: Mitigation actions taken in advance of 

drought will include conserving water, improving soil health, and taking 

advantage of and improving the storage capacity of wetland and riparian 

areas. Response actions will include instream flow minimums at key 

locations that will trigger water conservation measures. 

The process will include tying together the drought plans in the individual 

watersheds. This is especially important for watersheds such as the Jefferson 

River basin, where river flows depend on contributions from upstream tributaries, 

in this case the Big Hole, Ruby, and Beaverhead Rivers. 

Evaluation and updating the plan will be ongoing and include testing the 

effectiveness of the plan under simulated drought conditions. Drought 

characteristics will be selected that are most relevant and problematic, including 

single-year and multi-year droughts and late season “flash” droughts. An iterative 

process could be used and the impacts to resources could be reassessed with the 

mitigation and response actions in place and subsequently adjusted as appropriate. 
Missouri Headwaters Basin Study

123

6.10.3. Performance 

The Big Hole River basin provides an example of how a group can work to build 

drought resilience through a coordinated long-term effort that includes all 

stakeholders. The plan includes voluntary conservation targets for all water users 

and relies on shared sacrifice for shared success. It encourages irrigation and 

stock water conservation during drought, and fishing restrictions when drought 

conditions reach critical levels. As an example, Table 18 provides a synopsis of 

flow targets from the Big Hole River Drought Management Plan for the upper 

portion of the Big Hole River basin at the USGS Big Hole River below Lake 

Creek at Wisdom gauge (USGS gauge #06024450). In addition to the actions 

listed, late afternoon and evening fishing restrictions are also implemented when 

river temperatures exceed 73 °F for three consecutive days. 

Many Big Hole River water users have 

committed to maintaining these targets 

through Candidate Conservation 

Agreements with Assurances (CCAA). 

These agreements between (USFWS and 

property owners who voluntarily agree to 

manage their lands and resources to 

remove threats to species at risk of 

becoming threatened or endangered and 

who in turn receive assurances against 

additional regulatory requirements should 

that species be subsequently listed under 

ESA. The CCAA’s conservation goal for 

the Big Hole River is to secure populations 

of the native fluvial (river-dwelling) Arctic 

grayling. In 2014, the USFWS found that this distinct population segment in the 

Upper Missouri River basin does not warrant protection under the ESA, due 

largely to significant conservation efforts in the past decade such as the Big Hole 

River Drought Management Plan. 

Figure 33 compares gaged summer flows during 1988, before the flow targets and 

other conservation measures in the Big Hole River Drought Management Plan 

were adopted, to modeled streamflow with the targets. Maintaining these targets 

does come with certain costs to other resources, primarily as some production of 

irrigated hay crops reductions that result from irrigation water shortages. 

Figure 34 is a synopsis of changes to resource benefits associated with three latesummer targeted instream flow rates across projected future climate scenarios and 

paleo event scenarios. This strategy explores the effects of the various instream 

flow targets listed in Table 18 but does not capture the dynamic and voluntary 

nature of the targets. Thus, this strategy helps to understand the sensitivity of 

irrigation water shortage and summer flow to these targets if they were invoked. 

Big Hole River watershed Arctic grayling.
6. Strategies

124

Table 17.—Summary of Flow Targets for the Big Hole River below Lake Creek at 

Wisdom Gage 

Target Action when flow reaches at or below target

April 1 - June 30

160 cfs Water users with conservation plans will implement them. Others will be 

contacted and encouraged to implement conservation measures. The 

goal of this target is to maintaining spawning and rearing flow 

requirements for Arctic grayling. 

July 1 - October 31

60 cfs Montana DNRC and Montana DFWP officials will work with the Big Hole 

Watershed Committee to formulate options and prepare to act. This 

could include conservation plan implementation, voluntary reduction of 

irrigation and stock water diversions, municipal water use, angling, and 

encouragement of the use of stock watering wells. A phone tree will be 

used to notify water users and outfitters and anglers of low water 

conditions and encourage conservation measures. Information will be 

posted online and on social media platforms.

40 cfs A phone tree will be used to provide notice to outfitters and anglers 

requesting they voluntarily limit their angling activities to earlier, cooler

hours of the day. Water users will be asked to contact other water users 

and encourage water conservation. The Big Hole Watershed Committee 

will contact the media to inform public of low flow conditions.

Information will be posted online as well as on social media platforms.

20 cfs Montana DFWP will close the upper section of the Big Hole River to

fishing and encourage public conservation efforts. The phone tree will be 

used to contact water users and outfitters/anglers to advise them about 

the river closure and extreme low water conditions and to encourage 

conservation measures. Information will be posted online on the Big Hole 

Watershed Committee (BHWC) website (http://www.bhwc.org/), via 

BHWC social media platforms, and on the Montana DFWP website.
Missouri Headwaters Basin Study

125

Figure 33.—Modeled flows for Big Hole River near Wisdom gage compared to the 

historical gaged flow.

Missouri Headwaters Basin Study

127

Figure 34.—Resource comparison grid for Water Management Strategy for Increased Drought Resilience strategy. (2050s futures). 

Missouri Headwaters Basin Study

129

Figure Orientation

In Figure 34, the percent change in performance measures, shown in the large 

upper panels, under different future and paleoclimate scenarios as well as with 

different strategies are presented relative to the historical baseline—which uses 

historical climate conditions, existing system configuration, and existing system 

operating rules. These changes are shown on the figures both as colors—

increasingly dark red for negative changes, and increasingly dark green for 

positive changes—and arrows indicating the direction of change—an up arrow 

(△) for positive change and a down arrow (▽) for negative change. If changes, 

positive or negative, are less than five percent, they are shown as no change. If 

changes, positive or negative, exceed one hundred percent, they are shaded as 

plus or minus one hundred percent and marked with a dot (•). 

The left panel shows performance under future and paleoclimate scenarios 

without strategies (baseline). The HD, HW, CT, WD, and WW future scenarios 

are shown along with the MID, LDP, MIP, and LP paleoclimate scenarios. This 

suggests how climate alone will impact system performance and identifies 

vulnerabilities under a range of different scenarios. Including both the future and 

paleoclimate scenarios also shows how the range of projected future change 

compares to historical variability. The reader may explore in these figures: do the 

future scenarios stay within the range of the paleoclimate scenarios, or do they 

exceed it, and in what measures? 

The middle panel shows how different strategies affect the performance measures 

under historical conditions. The reader may explore in these figures: had the 

strategy been implemented under current conditions, what effect does it have? 

The third panel shows the effect of strategies under future and paleoclimate 

scenarios. The reader may explore in these figures: do the strategies have a 

noticeable effect on the vulnerabilities identified in the first panel, and are the 

effects of the strategies seen under historical conditions in the second panel still 

evident under a range of scenarios? 

Figure Discussion

In the future, especially under the hotter and drier scenarios, the streamflow 

targets could be expected to be more important in maintaining aquatic resources 

in this section of the river. The chart also shows increases in irrigation water 

shortages for future scenarios, although these primarily are attributed to changes 

in crop demands and flow conditions for the future scenarios rather than the 

streamflow targets.
6. Strategies

130

6.11. Strategies Considered but not Evaluated

This section summarizes strategies that were identified during the Basin Study 

process but not further pursued. 

6.11.1. Shift Drawdown Operations Timing at Canyon Ferry Reservoir

and Lake Elwell

Most future scenarios project an earlier shift of runoff inflow to Canyon Ferry 

Reservoir and Lake Elwell and projected higher peak inflow during wetter years. 

A potential strategy would be to shift the timing of reservoir flood control 

operations to earlier in the season for years with high projected runoff. The 

strategy was not pursued further because of the complexity of flood control 

operations associated with these Missouri reservoirs in conjunction with other 

Mainstem Missouri River reservoirs and the USACE. This is a strategy that could 

be pursued in the future, with input from USACE. 

6.11.2. Beaverhead Valley Aquifer Recharge

This strategy would use existing infrastructure, such as the East Bench Canal, to 

recharge shallow aquifer storage in the lower Beaverhead Valley for later 

withdrawal to ease late-season irrigation water shortages through supplemental 

groundwater pumping. The strategy was not pursued further because initial model 

runs indicated that there are only short, infrequent periods of time when water is 

available to recharge groundwater. Typically, during spring runoff when water is 

most likely to be available, all flow above senior rights is needed to fill Clark 

Canyon Reservoir. The few years when this water is available tend to be higher 

flow years when late-season supplemental groundwater pumping is less likely to 

be needed. Due to the nature of the aquifer and relatively short distances from the 

Beaverhead River, little aquifer recharge water was modeled to be carried over 

from one season to the next. 

6.11.3. Flushing Flow Releases from Clark Canyon Reservoir

The Beaverhead River below Clark Canyon Reservoir is a valuable trout fishery. 

Maintaining the quality of this fishery requires not only water, but a clean gravel 

streambed substrate that provides habitat for the aquatic insects that trout feed on 

and allows for trout to successfully spawn. Periodically, during times of low 

releases from Clark Canyon Reservoir, spring storms in downstream tributary 

drainages, primarily Clark Canyon Creek, will introduce high loads of sediment 

into the Beaverhead River. Higher flows are required to mobilize these sediments 

and flush them out of the gravel bed substrate. Reclamation completed a sediment 

flushing flow study and model (Reclamation 2013) that predicted that flows of 

600 cfs would be needed to mobilize river bed gravels and remove the fine 

sediments. Further work by Applied Geomorphology (2014) recommended the 

duration and ramp-up and ramp-down rates for flushing flow releases. A 

successful flushing flow release that followed these recommendations was made 
Missouri Headwaters Basin Study

131

during May 2017, with a total of 2,091 acre-feet released. The strategy was not 

analyzed further because these releases already are being implemented through 

the cooperation of the East Bench Unit Joint Irrigation Board, Reclamation, 

Montana DFWP, and Beaverhead Watershed Committee. 

6.11.4. Musselshell River Basin Off-Stream Reservoir Fill Sequencing 

Change

There are two existing off-stream storage reservoirs in the Musselshell River 

basin: Martinsdale and Deadman’s Basin Reservoirs. Because water rights 

associated with Deadman’s Basin Reservoir are senior to those for Martinsdale 

Reservoir, it typically has priority in filling. At times, this priority order can 

restrict the filling of Martinsdale Reservoir. An option was preliminarily assessed 

that would look at the implications of filling Martinsdale Reservoir in priority 

before Deadman’s Basin Reservoir. Model results showed potential decreases in 

basin-wide irrigation water shortages during drier years, but there was no 

discernable pattern that could be used to predict when a filling sequence change 

would be advantageous.

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7. Next Steps and Future Considerations 

This report has described some of the projected future water resources challenges 

and opportunities for the Missouri River Headwaters. Although total basin water 

supplies are projected to increase under most future scenarios, as measured by 

average annual flow volume, streamflow during the critical late-summer season 

are projected to decrease on many streams under most scenarios. At the same 

time, the amount of water consumed by irrigated crops (evapotranspiration) and 

that which evaporates from reservoirs is projected to increase under most 

scenarios. As the population in the study area continues to grow, more water will 

need to be provided for municipal and domestic needs, and economic 

development. Despite these challenges, the Basin Study describes some

opportunities for future adaptation. 

There still is water available for contract from Canyon Ferry Reservoir and Lake 

Elwell to meet future needs while minimizing impacts to other resources, and 

there may be some flexibility with how these dams can be operated in the future. 

The United States has determined that a water supply can be made available to 

water contractors without significantly impacting existing or future authorized 

purposes of the Canyon Ferry Unit and Lower Marias Unit of the Pick-Sloan 

Missouri Basin Program. Any future additional contracted water may be subject 

to restrictions in drought conditions. Most scenarios project increased future 

annual runoff volumes into these reservoirs, some of which might be available to 

capture and store for later use. The stored water might provide for new 

consumptive uses, such as irrigation, or could be used to enhance ecological flow 

releases. Finally, watershed groups and conservation districts are active in the 

Missouri Headwaters and provide an opportunity to develop and implement 

adaptive water management strategies at the local level, such as for drought 

planning. 

The following are some next steps that might be taken to improve the Upper 

Missouri RiverWare planning mode and apply it to existing and potential future 

water resources problems. Also included are steps that Reclamation and Montana 

DNRC can take to continue to promote the collaboration and water resources 

planning in the basin—which is key to implementing strategies. 
7. Next Steps a

134

7.1. Potential Future Applications of the Upper Missouri 

RiverWare Planning Model

• Examining alternative strategies for early season reservoir draw-down 

operations in the future given the potential for higher runoff volumes. 

• Using the Upper Missouri RiverWare planning model structure and results 

to inform and enhance current operational models for Reclamation 

reservoirs. This could include those for the Beaverhead River basin, Sun 

River basin, and Canyon Ferry Reservoir and Lake Elwell. 

• Facilitating the analysis of water contracting from Reclamation reservoirs, 

such as at Canyon Ferry and Lake Elwell. 

• Facilitating the implementation of water rights compacts, such as those for 

the Blackfeet Tribe and Chippewa Cree Tribe-Montana Compact. 

• Analyzing areas where irrigation efficiency improvements might have the 

potential to provide multi-resource benefits. 

7.2. Potential to Update Models

• Expand and update the naturalized streamflow data set for the major 

streams in the Missouri Headwaters to include through the year 2018. The 

current data sets only contain naturalized streamflow estimates through the 

late 1980s. In the meantime, there have been substantial changes to 

irrigation depletions and return flow characteristics that affect natural flow 

computation. Also, lengthening the data set would bring in the severe 

drought years of the early 2000s and the notable 2011 and 2018 high flow 

years. 

• Improve upon hydrologic model, either through increased spatial 

resolution of the VIC model, or by exploration of additional modeling 

approaches. 

• Correspondingly, update the lake evaporation and ET demands models to 

include through the year 2018. This would include irrigation demands and 

reservoir evaporation rates.

• Run and calibrate the Upper Missouri RiverWare planning model for the 

historical data set through the year 2018. 

• Update the models to include any refinements made to projected future 

conditions. 
Missouri Headwaters Basin Study

135

7.3. Continued Collaboration and Support

The project partners developed or enhanced working relationships with many 

agency staff and groups during this Basin Study. This collaboration should be 

continued, such as through periodic attendance and presentation at watershed 

group meetings, and presentations at conferences of professional organizations. In 

addition, the project partners should continue to support, when resources allow, 

the work of watershed groups and conservation districts, especially for water 

management activities related to strategies.

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8. Uncertainty

The information presented in this report was developed in collaboration with 

basin stakeholders and was peer reviewed in accordance with the Bureau of 

Reclamation and Department of the Interior polices. This report is intended to 

inform and support planning for the future by identifying potential future 

scenarios. The analyses provided in this report reflect the use of best available 

datasets and methodologies at the time of the study. 

Water resources studies are developed in collaboration with basin stakeholders to 

evaluate potential future scenarios to assess risks and potential actions that can be 

taken to minimize impacts, including supply and demand imbalances. These types 

of studies support a proactive approach to water resources management, using the 

best available science and information to develop scenarios of future conditions 

within the watershed. This positions communities to take steps now to mitigate 

the impacts of future water supply management issues, including water shortages, 

impacts of droughts and floods, variations in water supply, and changing water 

demands for water for new or different uses. 

Because every water resources planning study requires the study partners to make 

assumptions about future conditions, addressing the uncertainties in those 

assumptions is an essential component of the planning process. For example, 

there are uncertainties associated with the characterization of future water supply 

and demand, demographics, environmental and other policies, economic 

projections, climate conditions, and land use, to name a few. Moreover, 

projections are often developed using modeling techniques that themselves are 

only potential representations of a particular process or variable, and therefore, 

introduce additional uncertainties into characterizations of the future. The 

cumulative, interacting uncertainties are not well known in the scientific 

community and, therefore, are not presented within this study. By recognizing this 

at each process step, uncertainties are adjusted for and reduced when possible, to 

allow Reclamation and its stakeholders to use the best available science to create 

a range of possible future risks that can be used to help identify appropriate 

strategies, which is fundamental to the planning process. Importantly, scenarios of 

future conditions should not be interpreted as a prediction of the future, nor is the 

goal of any water resources planning study to focus on a singular future. Rather 

the goal is to plan for a range of possible conditions, thereby providing decision 

support tools for water managers.

Missouri Headwaters Basin Study

139

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