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.
Acronyms and Abbreviations

Basin Study Missouri Headwaters Basin Study 

CT Central tendency future scenario

ESA Endangered Species Act

FSID Fort Shaw Irrigation District

GCM global climate models 

GID Greensfield Irrigation District

HD Hot-dry future scenario. 

HW Hot-wet future scenario 

Impacts Assessment Upper Missouri Basin Impacts Assessment

LD Longest Drought 

LP Longest Pluvial 

MID Most Intense Drought 

Montana DNRC Montana Department of Natural Resources and 

 Conservation 

MIP Most Intense Pluvial 

Reclamation Bureau of Reclamation 

USGS U.S. Geological Survey 

WD Warm-dry future scenario

WW Warm-wet future scenario

WaterSMART Water Sustain and Manage America’s Resources for 

Tomorrow

iii

Contents

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

Study Area and Existing Challenges ........................................................................................... 1

Basin Study Purpose and Development.................................................................................... 3

Uncertainty ........................................................................................................................................... 4

Collaboration and Outreach .......................................................................................................... 6

Scenarios and Analysis...................................................................................................................................... 7

Findings from the Impacts Assessment ................................................................................................... 10

Water Supply ..................................................................................................................................... 10

Water Demand .................................................................................................................................. 11

Risk Assessment ................................................................................................................................ 12

Strategies and Key Findings ......................................................................................................................... 15

Providing Water for Future Consumptive Uses through Contract Water from 

Canyon Ferry Reservoir and Lake Elwell ................................................................. 19

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

Gallatin Valley ................................................................................................................... 19

Increasing Canal and On-farm Irrigation Efficiencies ........................................................ 20

Ecological Flow Releases from Canyon Ferry Reservoir and Lake Elwell.................... 20

Beaverhead River Basin Strategies ............................................................................................ 21

Sun River Basin Strategies ............................................................................................................ 21

Musselshell River Basin Strategy ................................................................................................ 22

Water Management Strategy for Increased Drought Resilience .................................. 22

Next Steps............................................................................................................................................................ 23

References ........................................................................................................................................................... 27

Figures

Figure 1.—Missouri Headwaters Basin Study overview map. ........................................................... 2

Figure 2.—Overview of the Missouri Headwaters Basin Study and complementary 

Upper Missouri Basin Impacts Assessment. ........................................................................ 5

Figure 3.—Partnerships for the Missouri Headwaters Basin Study................................................. 6

Figure 4.—Illustration of scenario approach for Missouri Headwaters Basin Study ................ 8

Figure 5.—Summary of Impacts Assessment results by region. .................................................... 13

Figure 6.—Overview of strategy locations. ............................................................................................. 17

Tables

Table 1.—Risk Assessment Measures ....................................................................................................... 12

Table 2.—Key Findings ................................................................................................................................... 23

Missouri Headwaters Basin Study

Summary Report

1 

Introduction 

The Missouri Headwaters Basin Study (Basin Study) describes strategies to 

address water resource challenges in the Missouri River and Musselshell River 

basins upstream of Fork Peck Reservoir. 

These watersheds provide habitat for numerous fish and wildlife species and 

supply water for agriculture, hydropower, recreation, and tribal, municipal, 

industrial, and domestic uses. Within 

this study area, the Missouri River and 

its tributaries are the primary water 

source for 320,000 people and about 

1.1 million acres of irrigated land. 

Study Area and Existing 

Challenges

The Basin Study area encompasses the 

Missouri River and Musselshell River 

basins upstream of Fort Peck Reservoir, 

covering about 50,000 square miles 

(Figure 1). The Jefferson, Madison, and 

Gallatin Rivers, which originate in 

southwestern Montana in the Rocky 

Mountains, join to become the Missouri 

River near the town of Three Forks. Further 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 River basins, which drain to 

the Missouri River downstream of Great Falls. The study area also includes the 

extensive tributary drainage of the Musselshell River basin, which drains directly 

into Fort Peck Reservoir. The combined watersheds have an annual average 

outflow of about 6.7 million acre-feet. 

Missouri Headwaters Setting

State: Montana 

Major Cities: Bozeman, Helena, Great Falls

Mean Annual Flow: 6.7 million acre-feet

Basin Study Area: 50,000 square miles

Major Water Uses: Municipal, agriculture, 

hydropower, recreation, flood control, 

navigation, fish and wildlife

Notable Reclamation Facilities: Pick-Sloan 

Missouri Basin Program, including East Bench 

Unit, Crow Creek Pump Unit, Canyon Ferry 

Unit, Helena Valley Unit, Lower Marias Unit, 

Sun River Project
Missouri Headwaters Basin Study

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Figure 1.—Missouri Headwaters Basin Study overview map.
Missouri Headwaters Basin Study

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The study area stakeholders face challenges similar to those in other watersheds in 

the western United States where finite water supplies serve increasing demands. 

The greatest demand in the study area is for irrigation, comprising about 

87 percent of the total consumptive water demand. Reservoir evaporation 

accounts for about 12 percent and all other uses about 1 percent (Montana 

Department of Natural Resources and Conservation [Montana DNRC] 2014). In 

the study area, most of the water has already been appropriated for irrigation, 

hydropower generation, municipal water supply, and instream flows to support 

fisheries and recreation. 

To illustrate the effects of limited water supply in the region, the Missouri River 

basin upstream of Great Falls has been closed to new water appropriations since 

1993, with some exceptions for groundwater and water storage. Irrigators in this 

region, and in the Musselshell, Sun, and Teton River basins have already 

experienced water shortages. Rapid population growth in the study area over the 

past 20 years is expected to continue and will require additional water for 

municipal water supplies mostly concentrated in Gallatin, Madison, and Lewis 

and Clark Counties in southwestern Montana. For example, annual water demand 

in Gallatin County is expected to at least double by 2080. Currently, unallocated 

stored water that the Bureau of Reclamation (Reclamation) manages remains in 

Canyon Ferry Reservoir and Lake Elwell (Tiber Dam)—offering the potential for 

mitigation against future hydrologic change and for meeting demand for 

additional water to support both expanded irrigation and population growth. 

Another challenge in the region is that hydropower producing facilities on the 

Missouri River have relatively senior water rights. On top of that, rivers 

throughout the study area hold instream flow rights to support Endangered 

Species Act (ESA) listed species such as the Pallid sturgeon, and species of 

special concern such as the fluvial Arctic grayling and west-slope cutthroat trout, 

as well as renowned trout fisheries of the Big Hole, Gallatin, Beaverhead, 

Jefferson, Madison, Smith, and Missouri Rivers. Use by senior water rights 

holders and instream flow needs leave little flexibility for junior water rights 

holders to divert water in many parts of the study area. Rivers and reservoirs in 

the Missouri Headwaters, such as the Missouri and Madison Rivers and Canyon 

Ferry Reservoir, provide some of the highest value recreation areas in Montana. 

Basin Study Purpose and Development

Reclamation and the Montana DNRC undertook this Basin Study. The purposes 

of this collaborative planning study are to inform stakeholders of current and 

future water supply challenges and to identify and evaluate strategies for 

improving resiliency to these challenges and for improving water supply 

reliability. Strategies include actions like changing current management practices, 

changing operations, and modifying or developing new infrastructure.
Missouri Headwaters Basin Study

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Uncertainty

The information presented in this report was developed in collaboration with 

basin stakeholders and was peer reviewed in accordance with Reclamation’s and 

Department of the Interior’s 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 

adaptation 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. 

The Basin Study builds upon the Upper Missouri Basin Impacts Assessment 

(Impacts Assessment) (Reclamation 2019c), which summarizes current and future 

water resource challenges identified through modeling of the managed river 

system under a range of water supply and demand scenarios. Unlike many 

completed basin studies, the foundational Impacts Assessment is summarized in a 

separate report completed by Reclamation, in cooperation with the Montana 

DNRC. In the Impacts Assessment, Reclamation developed a scenario approach 

for modeling water supply and demand. These scenarios include: future climate 
Missouri Headwaters Basin Study

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5 

projections at the watershed scale based on global climate model (GCM) output, 

paleohydrology scenarios generated from tree rings that provide information from 

the distant past (Martin and Pederson 2019), and a historical scenario that 

encompasses the observed historical record. Information from this range of 

scenarios facilitates comparisons between the past and future projections of water 

supply and demand and can provide information as to whether future water supply 

and demand are likely to be significantly different from the past. In addition to 

assessing water supply and demand, Reclamation and the Montana DNRC also 

collaborated to develop the Upper Missouri RiverWare planning model 

(Reclamation 2019b), which is the tool used to simulate the river system and 

quantify impacts to metrics for water delivery, water quality, flood control, 

threatened and endangered species, flow-dependent ecological resiliency, and 

recreation. 

This Basin Study summarizes an analysis of how management and infrastructure 

changes may alleviate any identified water resources challenges moving forward. 

With stakeholder input, Reclamation and Montana DNRC developed strategies to 

mitigate water supply and demand challenges and evaluated them based on their 

ability to meet the same metrics described above. Further, the Basin Study 

provides information that can 

support managing available water 

resources in the basin, 

considering existing challenges, 

growth, and projected future 

changes to water supplies and 

demands. 

Figure 2 illustrates the 

components of the Basin Study 

(shaded beige) and their 

connections with components of 

the Impacts Assessment (shaded 

blue). It illustrates the concept 

that the Basin Study builds on 

information developed through 

the Impacts Assessment and 

focuses on strategies for 

addressing projected changes in 

water supply and demand. 

Figure 2.—Overview of the Missouri Headwaters Basin 

Study and complementary Upper Missouri Basin 

Impacts Assessment.
Missouri Headwaters Basin Study

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Collaboration and Outreach

Basin Studies costs are equally shared between Reclamation and non-Federal 

partners. Reclamation and Montana DNRC were partners in this Basin Study. In 

addition, Reclamation contracted with the U.S. Geological Survey (USGS) 

Northern Rocky Mountain Science Center and Montana State University, 

Bozeman to develop paleohydrology scenarios (Martin and Pederson 2019) for 

the Impacts Assessment and Basin Study and provide guidance for their 

application (Figure 3). In addition, collaboration and outreach with stakeholders 

and tribes are key components of these studies. 

Reclamation and Montana DNRC 

engaged with stakeholders in the study 

area to develop management strategies. 

Stakeholders included members of local 

watershed groups and conservation 

districts who are knowledgeable and 

active in local water resource issues. These groups include: Sun River Watershed 

Group, Musselshell Watershed Coalition, Beaverhead Watershed Committee, 

Ruby Watershed Committee, Liberty County Conservation District, Montana 

DNRC State Water Projects Bureau, East Bench Irrigation District, Helena Valley 

Irrigation District, and Great Northern Landscape Conservation Cooperative. 

Additionally, the study team contacted the Blackfeet Tribe Water Resources 

Director by personal communication at the start of the study to identify possible 

strategies related to tribal water rights and their use. The Blackfeet Tribe was in 

the process of finalizing their water right settlement by holding a Tribal 

referendum to approve the settlement. During this time, the Tribe identified no 

strategies, but one evaluated strategy in the study explored additional water use 

from Lake Elwell in the Marias River basin—which may be beneficial to the 

Figure 3.—Partnerships for the Missouri Headwaters Basin Study.

Stakeholder involvement was 

critical in developing strategies 

and assessing the strategy benefits. 
Missouri Headwaters Basin Study

Summary Report

7 

Tribe’s Lake Elwell allocation per their water rights settlement with the Federal 

government. 

Another important component of each basin study is collaboration with other 

ongoing efforts in the study area. The study team collaborated with efforts 

including the National Drought Resilience Partnership Montana Pilot Project and 

the Missouri Headwaters WaterSMART1 drought contingency planning process. 

Scenarios and Analysis

The Basin Study and the foundational Impacts Assessment incorporate newly 

developed data and tools to quantify water supply and demand and for evaluating 

strategies. Reclamation and Montana DNRC used a scenario approach, which is 

described in detail in the Impacts Assessment, to develop water supply and 

demand data for a range of plausible conditions. These data were then input into 

the developed Upper Missouri RiverWare planning model for simulation and 

analysis. 

Water supply scenarios may be described as scenarios of streamflow, reservoir 

inflows, and local inflows that are simulated by hydrologic and statistical models. 

Groundwater and surface water interactions were modeled by altering surface 

water flows based on aquifer characteristics.

Water demand scenarios may be described as scenarios of evaporative demands 

from reservoirs and agricultural demands via crop evapotranspiration; they also 

incorporate population estimates for municipal and industrial water use. 

Scenarios of water supply and demand encompass three types: paleohydrology 

(spanning years 1100 to 1998), historical baseline (encompassing years 1950 to 

1999), and projected future scenarios under three planning horizons: the 2020s 

(which encompasses years 2010 - 2039), the 2050s (which encompasses years 

2040 - 2069), and the 2080s (which encompasses years 2070 - 2099). 

Figure 4 illustrates the scenarios developed for the Basin Study showing the 

variability in streamflow under different scenarios. 

1 WaterSMART stands for Sustain and Manage America's Resources for Tomorrow. 
Missouri Headwaters Basin Study

Summary Report

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Figure 4.—Illustration of scenario approach for Missouri Headwaters Basin Study. 

Details of the different scenario types are provided below. 

• Paleohydrology. Paleohydrology was developed from tree-rings to 

provide a record of hydrologic conditions over the past 900 years, from 

about 1100 to 1998 (Martin and Pederson 2019). The study team 

developed daily streamflow timeseries over 50-year periods that 

encompass either extreme drought periods or extreme wet periods (also 

called pluvial periods), identified from tree rings-collectively. These daily 

streamflow timeseries were used in two unique ways: 

o By identifying the longest wet period (termed longest pluvial 

[LP]), the period with the most intense wet period (termed most 

intense pluvial ([MIP]), the period with the most intense drought 

(MID), and the longest drought (LD) in the paleohydrology record 

and used these as paleohydrology scenarios—collectively, these 

are called “extreme paleo events.” 

o By combining the streamflow sequences and event durations from 

the extreme scenarios described above with projected streamflow 

from future scenarios (described below)—these are called “future 

scenarios combined with paleohydrology.” 

• Historical simulations. The Basin Study simulated the historical baseline 

period from 1950 to 1999 (water years 1951 - 1999) to represent historical 

hydrologic conditions over that period. 
Missouri Headwaters Basin Study

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9 

• Future scenarios. Future scenarios based on GCM projections were 

developed and provide our best estimate of what could occur over the 

coming century with respect to climate dynamics and warming. For this 

study, each scenario for a particular time horizon is considered an equally 

likely future planning scenario. These scenarios include five climate 

timeseries developed for the region that represent the range of projected 

changes in temperature (less warming to more warming) and precipitation 

(from decreases to increases) for three future time horizons, the 2020s, the 

2050s, and the 2080s and these are called warm-wet (WW), hot-wet 

(HW), a middle range central tendency (CT), warm-dry (WD), and hot-dry 

(HD).

For these scenario types, the study team 

used the Upper Missouri RiverWare 

planning model to simulate river and 

reservoir operations, with and without 

strategies in place, and assuming 2017 

operating policies. Model results 

provide information on agricultural 

water deliveries, managed river flows, 

and reservoir levels. The study team 

compared results from future scenarios 

to both historical baseline simulations 

and to paleohydrology scenario 

simulations to answer whether projected 

future conditions may be outside the 

range of conditions seen over the last 

900 years. 

The analyses provided in this report 

reflect the use of best available datasets 

and data development methodologies at the time of the study. It is important to 

acknowledge the uncertainties inherent within projecting future planning 

conditions for water supply and demand. For example, projections of future 

climate, population, water demand, and land use contain uncertainties that vary 

geographically and temporally depending on the model and methodology used. 

Trying to identify an exact impact at a particular place and time remains difficult, 

despite advances in modeling efforts over the past half-century. Accounting for 

these uncertainties, Reclamation and its stakeholders used a scenario planning 

approach that encompasses the estimated range of future planning conditions. 

More detailed information about uncertainties related to each part of the study is 

available in the Missouri Headwaters Basin Study full report. 

Upper Missouri RiverWare Planning Model excerpt.
Missouri Headwaters Basin Study

Summary Report

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Findings from the Impacts Assessment

The Impacts Assessment summarizes how water supply and demand under 

paleohydrology scenarios and projected future scenarios may be different from 

recent historical conditions. It also summarizes how various categories of water 

use (water deliveries, hydroelectric power resources, flood control operations, 

ecological resources, and recreation) may change under these scenarios compared 

with recent historical conditions. These water use categories were examined 

through simulations of the Upper Missouri RiverWare planning model. This 

assessment also provides valuable context about whether managed resources 

under future scenarios face conditions never experienced in the recent or distant 

past. Key findings from the Impacts Assessment are summarized in this section to 

provide an understanding of impacts to water resources under various scenarios, 

without implementing any changes to operational policies or infrastructure. This 

information may serve as a foundation for later discussion of whether explored 

strategies may alleviate those impacts.

Water Supply 

Across the study area, annual water supply is 

projected to increase under most future 

scenarios compared to recent history. 

Projections generally show decreases in snowpack

(especially in high elevation parts of the Rocky 

Mountains), a shift to earlier peak snowpack, and 

thus earlier snowmelt driven runoff. 

Projected changes in the seasonality of water 

supply may leave areas more vulnerable to 

flooding during winter and spring seasons and 

water supply shortages late in the irrigation season. Projected future warming 

will shift spring snowmelt toward earlier in the year, causing a shift in the timing 

of peak streamflow with increasing winter and early spring runoff and decreasing 

runoff later in the spring and summer. The shift in seasonal runoff will be most 

pronounced along the Rocky Mountains. The shift is not projected in lower 

elevation watersheds, such as the Judith River basin. During the late summer 

season, a critical period for irrigation, water supply is projected to decrease on 

many streams under most scenarios. However, there are exceptions to this 

projection in some regions. For example, the watersheds along the Rocky 

Mountains, the Beaverhead River basin, and Musselshell River basin may 

experience little change or even an increase in summer streamflow.

Flooding in the Sun River.
Missouri Headwaters Basin Study

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Looking back over the reconstructed paleohydrology record, analysis showed that 

the range of annual streamflow over the last 900 years is greater than the range 

over the historical scenario period (1950 - 1999). This is to be expected in part 

because of the larger number of years contributing to the range in addition to the 

known major drought and pluvial events not captured in the timeframe of the 

more recent historical period. Droughts and wet periods (pluvial events) spanning 

2 to 8 years are fairly common in the study area. Longer drought events lasting 

10 to 30 years do occur. For example, the Dust Bowl (15 years) spanned from 

1929 - 1943 and the Millennium drought (11 years) spanned from 

2000 - 2010, and longer duration droughts have occurred in the 

paleohydrology record. 

Water Demand

Analysis of historical and projected 

future demand shows that future 

warming in the study area will

cause overall increases in water 

demand, on top of increases in 

demand from expanded 

irrigation and population 

growth. In fast growing regions, 

particularly the Gallatin Valley, 

there remains little unallocated 

water left to support increased 

water demand associated with 

population growth. 

Also, water demands associated with crop water consumption

Helena Valley irrigation.

are projected to 

increase with warming temperatures particularly in summer months. Increases in 

water demands, along with increases in reservoir evaporation, generally 

result in decreased reservoir storage by the end of the irrigation season.

Seasonal shifts in water supply availability could affect current irrigation practices 

for both agriculture and municipal lawn watering. 

Projected increases in precipitation that are expected at other times of the 

year may offset some of these projected demands, but precipitation is 

projected to decrease in summer months, which will increase reliance on 

reservoir storage.
Missouri Headwaters Basin Study

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Risk Assessment

The Impacts Assessment follows a modeling framework for evaluating water 

supply and demand conditions in a changing climate (Reclamation 2019a). That 

framework is used to evaluate risks to water management in the future and to 

evaluate the ability to meet the needs of the many users in the study area. As part 

of that framework, the Upper Missouri RiverWare planning model was developed 

to simulate current river and reservoir operations in the Upper Missouri River and 

Musselshell River and allow for easy simulation of water supply and demand 

scenarios. From these model simulations, the study team performed an assessment 

of water management risks. The RiverWare model was used to compute risk 

assessment measures related to agricultural water deliveries, managed river flows, 

and reservoir levels, among other things, throughout the study area. Quantitative

measures are used to help bring to light certain imbalances in water supply and 

demand under current management policies. Measures also allow for exploration 

of strategies that may reduce those imbalances. These measures were identified 

based on input from study partners, stakeholders, and resource managers in the 

basin. Examples of measures are summarized in Table 1. 

Table 1.—Risk Assessment Measures

Measure Category Measure Description

Basin-wide Responses Change in the days of centroid of flow timing

Change in end of month reservoir storage

Change in annual reservoir inflow volume

Change in April-October reservoir inflow volume

Change in November-March reservoir inflow volume

Water Deliveries Change in end of water year reservoir storage

Change in irrigation supply shortages

Hydroelectric Power 

Resources

Change in annual hydropower production at State, 

Federal, and private facilities

Flood Control Operations Change in days per month exceeding reservoir flood 

pool (Canyon Ferry, Clark Canyon, Tiber)

Ecological Resources* Change in monthly streamflow

Change in the annual maximum 7-day streamflow

Change in the annual minimum 7-day streamflow

Change in streamflow percentiles (5th, median, 95th)

Recreation Change in median number of unusable days at boat 

ramps

*The ecological resources category includes: 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.

A summary of impacts related to the water use categories, and these measures, is 

provided in Figure 5. These impacts highlight the need for strategies to address 

potential impacts to system performance..
Missouri Headwaters Basin Study

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Figure 5.—Summary of Impacts Assessment results by region.

Missouri Headwaters Basin Study

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Strategies and Key 

Findings

In the Basin Study, study partners 

developed and evaluated 

strategies to address challenges

identified in the Impacts 

Assessment and to address issues 

identified by study partners and 

through stakeholder outreach. 

This section contains a brief 

description of the strategies 

selected for analysis. 

Because the Missouri Headwaters 

is such a large basin, not all 

adaptation strategies affect the 

entire basin. Many of the 

adaptation strategies included 

here are specific to the larger 

Missouri River tributaries. Figure 

6 lists the strategies by location. It 

is possible that strategies in 

different subregions may be 

implemented simultaneously 

without impacting each other. 

Each group of strategies is further 

described below. The strategies’ 

key findings are then summarized 

in Table 2 at the end of this 

section. 

Strategies were developed to 

address future water needs and to 

adjust future water infrastructure 

operations to changing hydrologic 

conditions. The adaptation 

strategies also address major 

issues identified by the project 

partners and various stakeholders. 

Strategies Evaluated

Providing Water for Future Uses

• Providing Water for Future Consumptive Use 

through Contract Water from Canyon Ferry 

Reservoir and Lake Elwell

Providing Water for Future Municipal, 

Domestic, and Industrial Uses in the Gallatin 

Valley

Increasing Canal and On-farm Irrigation 

Efficiencies

Ecological Flow Releases from Canyon Ferry 

Reservoir and Lake Elwell

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

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

Musselshell River Basin Strategy

• New Off-stream Storage in Lower Musselshell River 

Basin

Water Management Strategy for Increased 

Drought Resilience

Missouri Headwaters Basin Study

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Figure 6.—Overview of strategy locations.

Missouri Headwaters Basin Study

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Providing Water for Future Consumptive Uses through Contract 

Water from Canyon Ferry Reservoir and Lake Elwell 

Contracting unallocated stored water managed by Reclamation from Canyon 

Ferry Reservoir and Lake Elwell (on the Marias River) is one of the greatest 

opportunities in the study area for relieving water resources challenges. Much of 

the basin is closed to new appropriations and less water in the lower Missouri 

River at Virgelle and in the Marias River below Tiber Dam/Lake Elwell is 

expected, potentially reducing Federal and state hydropower production. 

Contracting additional Canyon Ferry and Lake Elwell water might provide 

one of the few opportunities available to meet future consumptive use 

demands while sustaining other important resources. Measures associated 

with this strategy would not be impacted more substantially depending on the type 

of scenario, future or paleohydrology. 

Providing Water for Future

Municipal, Domestic, and 

Industrial Uses in the 

Gallatin Valley

During most years, water is 

available for the Lower Gallatin 

River beyond the senior instream 

flow rights from April through 

early July which are set by

Montana Department of Fish 

Wildlife and Parks. However, 

during the driest years, there is 

little, if any, water available 

above these rights. Although 

substantial regulatory hurdles 

may exist, providing additional 

domestic water to the Gallatin 

Valley through surface and 

groundwater conjunctive use or transporting surface water from Canyon 

Ferry Reservoir, could meet demands without impacting local water 

conditions. However, an important consideration for this strategy is that irrigated 

acres were modeled to be retired to supply the water needs for the municipal and 

rural domestic growth. This would substantially reduce irrigated acres in the 

greater Gallatin Valley.

Canyon Ferry Dam.
Missouri Headwaters Basin Study

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Increasing Canal and On-farm Irrigation Efficiencies

Over the past 40 years, irrigated areas have been converting from gravity flood 

systems to sprinkler irrigation systems, and delivery systems have decreased 

losses, for example, by converting open ditches to pipelines. This strategy 

investigated the effects of further increasing on-farm irrigation efficiencies and 

conveyance efficiencies across the study area. 

Watersheds in the study area will be impacted to varying degrees by increased 

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. 

While irrigation water shortages could increase under future scenarios with 

warming temperatures, increased irrigation efficiencies could lessen the 

impact, with the largest shortage reductions under hotter future scenarios. Also, 

as irrigation systems become more efficient, opportunities might open to mitigate 

potential late-season streamflow reductions through refinements to reservoir and 

delivery system operations. However, further increasing irrigation efficiency 

would have some adverse effects too—August flows would decrease in streams 

across the study area and hydropower production would decrease by a modest 

amount. 

Ecological Flow Releases from Canyon Ferry Reservoir and Lake Elwell

Ecological pulse flow releases from Canyon Ferry and Tiber Dams might improve 

aquatic habitat in the Missouri and Marias Rivers, and potentially trigger pallid 

sturgeon spawning in the lower Missouri River. 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. 

Opportunities for ecological flow releases, which may also be thought of as 

pulse flows to benefit fish and wildlife habitat, will be similar or even greater 

in the future, since future scenarios suggest it is likely for the region to be 

wetter overall. The results for this strategy show that scenarios reflecting climate 

change alone would have a greater impact than the future scenarios combined 

with paleohydrology in that the projected wet periods would be wetter than those 

experienced in the distant past. 
Missouri Headwaters Basin Study

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Beaverhead River Basin Strategies

Irrigation water shortages are common in the 

Beaverhead River basin. 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. The following strategies 

could store more water in Clark Canyon 

Reservoir to increase irrigation allocations 

during dry years and possibly improve 

Beaverhead River instream flow: 

• Decrease drawdown of Clark Canyon 

Reservoir maintain higher storage to decrease irrigation water shortages 

and to improve summer flows 

• Provide a more consistent winter instream flow rate downstream of the 

dam through reducing the maximum winter releases 

These strategies together could allow for more carry-over storage in Clark 

Canyon Reservoir, thus making more water available for instream flow in 

late summer and resulting in fewer irrigation water shortages for the East 

Bench Irrigation District and Clark Canyon Water Supply Company users. Sun 

and Musselshell River basins strategies appear to show only modest ability to 

meet their goals. Paleohydrology scenarios suggest that a broader range of 

reservoir inflows is possible, meaning that there could be more substantially 

decreased allocations if extreme drought conditions were to recur. Under such 

scenarios, the strategy could alleviate negative impacts.

Sun River Basin Strategies 

A system of canals and off-stream reservoirs provide water to Sun River irrigation 

water users. All future scenarios project that irrigation water shortages will 

increase, reservoir end of water year storage will decrease, and Sun River August 

flows will decrease. Strategies considered in the Sun River basin include 

modifying existing infrastructure associated with the Greenfields Irrigation 

District (GID) and Fort Shaw Irrigation District (FSID)2 to reduce irrigation water 

shortages and improve the ability to meet instream flow requirements.

Infrastructure modifications include increased Willow Creek Feeder Canal and 

Pishkun Supply Canal capacity, as well as new off-stream storage facilities. There 

would be modest benefits in dry years, reducing irrigation shortages and 

increasing reservoir end of water year storage. There would not be any 

appreciable impacts on summer streamflow in the Sun River. 

2 No changes to Broken O Ranch irrigation infrastructure or management were modeled.

Clark Canyon Reservoir.
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Musselshell River Basin Strategy

The current severe water shortages in drier years in the lower Musselshell River 

basin are projected to increase under most future scenarios. A strategy to address 

these shortages is namely a new off-stream storage reservoir in the lower 

watershed would be constructed in Horse Creek Coulee with inflow from the 

Musselshell River through the Delphia-Melstone Canal. The reservoir would have 

the most significant benefits during moderate flow years when there are enough 

flows to store in the fall and supplement irrigation in the following spring. In dry 

years, the reservoir could provide supplemental irrigation water during the first 

year of a drought. 

A new off-stream storage reservoir would 

generally increase flows in the Musselshell 

River at Mosby during critical summer 

months. Flows would decrease during the fall 

and spring reservoir fill periods, but still meet 

required instream flow targets. Water shortages 

to lower Musselshell River irrigators would 

increase, and summer instream flows decrease 

in most future scenarios. Although the new 

reservoir would offer limited benefits on 

average, it would reduce irrigation shortages 

and improve instream flows during moderate Musselshell River. and low-flow years. 

Water Management Strategy for Increased Drought Resilience

Several ongoing efforts in the Missouri River basin are investigating the impacts 

of drought and developing strategies for drought resilience, including the 

2015 Montana State Water Plan, National Drought Resilience Partnership 

Montana Headwaters Drought Resiliency Project, and associated efforts through 

Reclamation’s drought contingency planning. 

This strategy investigates the impact of severe drought in the Big Hole River 

basin and investigates ongoing efforts by the National Drought Resilience 

Partnership and Reclamation to mitigate its impacts and how effective these 

efforts might be in the future. The concept is that voluntary instream flow targets 

for the purpose of water conservation during drought may lessen severe impacts 

on the range of uses as a whole. Although this is not a system-wide strategy, it is a 

demonstration strategy for addressing the need for greater drought resilience. 

Through the demonstration project for drought resilience in the Big Hole River 

basin, it appears that voluntary flexible instream flow targets could provide 

multiple benefits while at the same time not substantially impacting 
Missouri Headwaters Basin Study

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23

irrigation water users. Especially under the hotter and drier future scenarios,

instream flow targets could be more important in maintaining aquatic resources. 

Future scenarios suggest greater impacts to late summer streamflow than if paleo 

events were to reoccur. 

Next Steps

The Missouri Headwaters Basin Study provides foundational information on the 

security of water supplies in the region, both historically and looking ahead to the 

future. The information developed in this study may be used for further analysis 

and/or in depth study. 

For example, one key finding from this study is that future scenarios suggest 

higher overall streamflow volumes in the future and shifting of the seasonal peak 

flow in many subbasins toward earlier in the year. Additional strategies may be 

explored to examine alternative operations specifically to address these changes. 

This was not identified as a strategy among stakeholder groups but could be 

analyzed in the future. 

In another example, the Upper Missouri RiverWare planning model could be 

improved and used as an adaptive management tool for existing and potential 

future water resources problems. Further, the RiverWare model structure and 

results are already being used to inform and enhance current operational models 

for Reclamation reservoirs, such as in the Beaverhead River basin. This could be 

expanded to other parts of the study area. 

Table 2.—Key Findings

Strategy Impact Description

Providing Water 

for Future 

Consumptive 

Uses through 

Contract Water 

from Canyon 

Ferry and Lake 

Elwell

Additional contracts for stored water in Canyon Ferry 

Reservoir and Lake Elwell would cause streamflow and 

hydropower production to decrease downstream (more 

substantially below Lake Elwell). 

Additional contracts for stored water in Canyon Ferry 

Reservoir and Lake Elwell would result in increased irrigation 

and agricultural production.
Missouri Headwaters Basin Study

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Table 2.—Key Findings

Strategy Impact Description

Providing Water 

for Future 

Municipal, 

Domestic, and 

Industrial Uses in 

the Gallatin 

Valley

Providing additional domestic water to the Gallatin Valley 

could meet demands without impacting local water 

conditions. 

Increasing Canal 

and On-farm 

Irrigation 

Efficiencies

The Missouri Headwaters region would benefit the most by 

decreased irrigation water shortages, followed by the Rocky 

Mountain Front region and the Musselshell region.

August streamflow in the Missouri River at Toston and the 

Sun River at Simms would modestly decrease, Big Hole River 

at Melrose and the Musselshell River at Roundup would see 

greater decreases. Hydropower production at Canyon Ferry 

Dam and NorthWestern Energy facilities on the Missouri 

River would also decrease.

Ecological Flow 

Releases

Future ecological flow releases would be possible at least as 

frequently as under historical conditions, and potentially 

much more frequently under wetter future scenarios. 

Hydropower production would modestly decrease at Tiber 

Dam but other facilities would see little impact. Also, late 

summer flows in the Missouri River and Marias Rivers would 

not be noticeably impacted.

Beaverhead 

River Basin 

Strategies

Storing additional water in Clark Canyon reservoir would 

decrease drawdown for flood storage and increase end of 

water year storage in dry years. There would be little impact 

on winter streamflow in the Beaverhead River downstream 

of Clark Canyon Reservoir, even in dry years.

Sun River Basin 

Strategies

There would be modest benefits in dry years, reducing 

irrigation shortages and increasing reservoir end of water 

year storage. There would not be any appreciable impacts 

on summer streamflow in the Sun River.

Musselshell River 

Basin Strategy

A new storage reservoir would have modest benefits in dry 

years, reducing irrigation shortages and increasing 

streamflow in moderate to low-flow years. There would not 

be any appreciable impacts on summer streamflow in the 

Musselshell River.

Water 

Management 

Strategy for 

Increased 

Drought 

Resilience

Agricultural interests will likely be asked to provide more 

water to maintain instream flows in the future, although 

these increased contributions are not expected to increase 

irrigation water shortages.

Maintaining a minimum instream flow of 60 cfs will become 

more difficult under most future scenarios.
Missouri Headwaters Basin Study

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In addition, Reclamation, Montana DNRC, and other stakeholders could take 

steps to continue to promote the collaboration and water resources planning in the 

basin which is key to implementing strategies. Some of these include: 

• Consider using the model to facilitate the analysis of water contracting 

from Reclamation reservoirs, such as at Canyon Ferry Reservoir and Lake 

Elwell. 

• Consider using the model to facilitate the implementation of water rights 

compacts, such as those for the Blackfeet Tribe and Chippewa Cree TribeMontana Compact. 

• The project partners developed or enhanced working relationships with 

many agency staff and groups during this Basin Study. This collaboration 

could provide future benefits, such as through periodic attendance and 

presentation at watershed group meetings, and presentations at 

conferences of professional organizations. 

• The project partners could continue to support, when resources allow, the 

work of watershed groups and conservation districts, especially for 

adaptive water management activities.

Missouri Headwaters Basin Study

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References

Martin, J., and G.T. Pederson. (2019.) Paleohydrologic reconstructions of wateryear streamflow for 31 stream gaging sites in the Missouri River Basin 

with complete data for 1685 through 1977: U.S. Geological Survey data 

release. https://doi.org/10.5066/P9OYY6DN.

Montana Department of Natural Resources Conservation (Montana DNRC).

2014. Lower Missouri Basin Water Plan 2014. Prepared by Montana 

DNRC and the Lower Missouri River Basin Advisory Council. Helena, 

Montana. http://dnrc.mt.gov/divisions/water/management/docs/

state-water-plan/upper-missouri/river-basin-plan/

upper_missouri_basin_report_final.pdf.

Reclamation. (2019b). Upper Missouri Basin Impacts Assessment: RiverWare 

Model. Technical Memorandum No. 86-68210–2017-07. Denver, 

Colorado.

Reclamation. (2019c). Upper Missouri Basin Impacts Assessment: Summary 

Report. Denver, Colorado.