U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2008–1113

Analysis of Pulsed Flow Modification Alternatives, 

Lower Missouri River, 2005

1,200

1,800

2,400

3,000

3,600

JAN 1 MAR 1 MAY 1 JULY 1 SEPT 1 NOV 1

0

600

DISCHARGE, IN CUBIC METERS PER SECOND

SEC000

Run-of-the-river

reference

New water-control plan

reference

Analysis of Pulsed Flow Modification 

Alternatives, Lower Missouri River, 2005

By Robert B. Jacobson

Open-File Report 2008–1113

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2008

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Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested citation:

Jacobson, R.B., 2008, Analysis of pulsed flow modification alternatives, Lower Missouri River, 2005: U.S. Geological 

Survey Open-File Report 2008–1113, 14 p.
iii

Contents

Abstract...........................................................................................................................................................1

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

Purpose and Scope ..............................................................................................................................1

Acknowledgments................................................................................................................................1

Methods...........................................................................................................................................................1

Visualization of Model Results............................................................................................................3

Extracting Flow Pulses.........................................................................................................................3

Graphical and Statistical Analysis of Pulsed Flow Modification Alternatives ...........................5

Results .............................................................................................................................................................5

Summary........................................................................................................................................................14

References Cited..........................................................................................................................................14

Figures

1. Map showing Missouri River Basin, Lower Missouri River (LMOR), and locations 

discussed in the text ....................................................................................................................2

2–7. Graphs showing—

2. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile 

range of daily discharge exceedances for the run-of-the-river reference, new 

water-control plan reference, and the R25000 alternative, modeled for historical 

conditions 1898–1997 ..........................................................................................................6

3. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile 

range of daily discharge exceedances for the run-of-the-river reference, new 

water-control plan reference, and the R250F3 alternative, modeled for historical 

conditions 1898–1997 ..........................................................................................................6

4. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile 

range of daily discharge exceedances for the run-of-the-river reference, new 

water-control plan reference, and the HMU000 alternative, modeled for historical 

conditions 1898–1997 ..........................................................................................................7

5. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile 

range of daily discharge exceedances for the run-of-the-river reference, new 

water-control plan reference, and the HMU0F3 alternative, modeled for 

historical conditions 1898–1997.........................................................................................7

6. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile 

range of daily discharge exceedances for the run-of-the-river reference, new 

water-control plan reference, and the HMU0F0 alternative, modeled for 

historical conditions 1898–1997.........................................................................................8

7. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile 

range of daily discharge exceedances for the run-of-the-river reference, new 

water-control plan reference, and the HMU403 alternative, modeled for 

historical conditions 1898–1997.........................................................................................8
iv

8–9. Graphs showing—

8. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile 

range of daily discharge exceedances for the run-of-the-river reference, new 

water-control plan reference, and the HMU493 alternative, modeled for historical 

conditions 1898–1997 ...................................................................................................................9

9. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile 

range of daily discharge exceedances for the run-of-the-river reference, new 

water-control plan reference, and the SEC000 alternative, modeled for historical 

conditions 1898–1997 ...................................................................................................................9

Tables

1. Selected flow-regime alternative design parameters, indicators of ecological

benefits, and indicators of social-economic costs.................................................................4

2. Simple environmental flow components used in flow-regime analysis..............................5

3. Comparisons of early pulse magnitude distributions ...........................................................10

4. Comparisons of late pulse magnitude distributions..............................................................10

5. Comparisons of early pulse duration distributions ...............................................................11

6. Comparisons of late pulse duration distributions..................................................................11

7. Comparisons of days per year low-lying agricultural lands are affected by flows, 

early pulse, Nebraska City, Nebraska.....................................................................................12

8. Comparisons of days per year low-lying agricultural lands are affected by flows, 

late pulse, Nebraska City, Nebraska .......................................................................................12

9. Comparisons of days per year flood stage is exceeded April–June, St. Joseph, 

Missouri........................................................................................................................................13

10. Comparisons of minimum monthly storage levels in reservoir system .............................13
v

Conversion Factors

SI to Inch/Pound

Multiply By To obtain

Length

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

meter (m) 1.094 yard (yd) 

Area

square meter (m2) 0.0002471 acre 

square kilometer (km2) 247.1 acre

square meter (m2) 10.76 square foot (ft2) 

hectare (ha) 0.003861 square mile (mi2

) 

square kilometer (km2) 0.3861 square mile (mi2)

Volume

cubic kilometer (km3) 810713.2 acre-foot (ac-ft)

Flow rate

cubic meter per second (m3/s) 35.31 cubic foot per second (ft3/s)

cubic meter per second per day 

(m3/s/d)

35.31 cubic foot per second per day 

(ft3/s/d)
vi
Abstract

The graphical, tabular, and statistical data presented in 

this report resulted from analysis of alternative flow regime 

designs considered by a group of Missouri River managers, 

stakeholders, and scientists during the summer of 2005. This 

plenary group was charged with designing a flow regime with 

increased spring flow pulses to support reproduction and survival of the endangered pallid sturgeon. Environmental flow 

components extracted from the reference natural flow regime 

were used to design and assess performance of alternative 

flow regimes. The analysis is based on modeled flow releases 

from Gavins Point Dam (near Yankton, South Dakota) for nine 

design alternatives and two reference scenarios; the reference 

scenarios are the run-of-the-river and the water-control plan 

implemented in 2004. The alternative designs were developed 

by the plenary group with the goal of providing pulsed spring 

flows, while retaining traditional social and economic uses of 

the river. 

Introduction 

A group of managers, stakeholders, and scientists 

(Missouri River Plenary Group, hereafter referred to as the 

plenary group) met during the summer of 2005 to design a 

more naturalized flow regime for the Lower Missouri River. 

The plenary group consisted of representatives of many 

interests on the Missouri River, including Federal and State 

Government agencies, Native American Tribes, and groups 

representing agriculture, navigation, public water supply, 

hydroelectric power, and environmental interests. The 

primary objective for a new flow regime was to support 

reproduction and survival of the endangered pallid sturgeon, 

Scaphirhynchus albus, while minimizing negative effects to 

social and commercial benefits of present river management. 

Specific flow-regime requirements for pallid sturgeon reproduction are unknown; therefore, much of the design process 

was based on features of the natural flow regime. The U.S. 

Geological Survey (USGS) facilitated the design process by 

developing tools to visualize, extract, and analyze Environmental Flow Components (EFCs) from simulation model outputs. Analyses were completed for two reference flow regimes 

and for nine design scenarios developed by the plenary group. 

Purpose and Scope

The purpose of this report is to act as a repository for 

graphical and tabular results of the analysis of alternative flow 

regimes. The materials are intended to provide support for 

extended interpretations and analyses published elsewhere. 

This analysis focuses on modeled flow releases from 

Gavins Point Dam (fig. 1) for two reference scenarios and 

nine alternative designs (table 1). The reference scenarios 

are the run of the river (ROR) and the new water-control 

plan (NWCP) implemented in 2004 (U.S. Army Corps of 

Engineers, 2006a). The alternative scenarios were developed 

by the plenary group with the objective of providing pulsed 

spring flows while retaining traditional social and economic 

uses of the river. Flow regime time series were developed by 

the U.S. Army Corps of Engineers using the Missouri River 

daily routing model (DRM) (U.S. Army Corps of Engineers, 

1998). This report is limited to visualization and analysis of 

outputs of the DRM model for the reference and alternative 

flow regimes.

Acknowledgments

Daily routing model output files were provided by Roy 

McAllister and Michael Swenson, U.S. Army Corps of 

Engineers, Northwestern Division, Omaha, Nebraska. 

Methods

The input to this analysis consisted of output of the DRM 

for modeled flow-regime scenarios. The DRM synthesizes 

Lower Missouri River (LMOR) discharge based on historical data for tributary inflows, calculations of streamflow 

depletions from evapotranspiration and consumptive use, and 

modifications of reservoir outflows according to water-control 

rules. The model simulates how reservoirs would be managed 

with a set of water-control rules, given the actual range of 

Analysis of Pulsed Flow Modification Alternatives, 

Lower Missouri River, 2005

By Robert B. Jacobson
2 Analysis of Pulsed Flow Modification Alternatives, Lower Missouri River, 2005

110°0'0"W 100°0'0"W 90°0'0"W

45°0'0"N

40°0'0"N

Base from U.S. Geological Survey digital data

Albers Equal-Area Projection

0 100 200 400 Kilometers

0 100 200 400 Miles

SASKATCHEWAN

ALBERTA

MONTANA

IOWA

KANSAS

WYOMING

COLORADO

NEBRASKA

MISSOURI

SOUTH

DAKOTA

NORTH

DAKOTA

Lake Oahe

Fort Peck Lake

Lewis & Clark Lake

Lake Sakakawea

Lake Francis Case

Lake Sharpe

Yellowstone River

Missouri River

Platte River

Missouri

River

Bismarck

Pierre

Sioux

City

Omaha

Kansas

City

St. Louis

Dam location

Major cities

Missouri

River

#

# #

#

#

#

#

MISSOURI

KANSAS

ARKANSAS

IOWA

ILLINOIS

NEBRASKA

SOUTH DAKOTA

Hermann

Nebraska City

Omaha

Kansas

City

Gavins Pt.

Dam

Ft. Randall

Dam

St. Louis

Sioux

City

Boonville

St. Joseph

Yankton

Ponca

# Gaging stations

Other locations

100°0'0"W 96°0'0"W 92°0'0"W

42°0'0"N

38°0'0"N

0 100 200 Kilometers

0 50 100 200 Miles

Base from U.S. Geological Survey digital data

Universal Transverse Mercator, zone 15

A

Base from U.S. Geological Survey digital data

Albers Equal-Area Projection

B

Figure 1. Map showing Missouri River Basin, Lower Missouri River (LMOR), and locations discussed in the text. 
Methods 3

variability of historical inflow data. Historical data are available, or have been estimated, for the period 1898–1997. The 

DRM uses these data and water-control rules to generate 100 

years of daily flows for 14 locations on the mainstem Missouri 

River. The 14 locations consist of nine streamflow-gaging stations on the Lower Missouri River and five streamflow-gaging 

stations in inter-reservoir river segments. This analysis focuses 

on evaluation of alternative flow regimes at Sioux City, Iowa, 

125 kilometers (km) downstream from Gavins Point Dam and 

at additional sites downstream at Nebraska City, Nebraska, 

and St. Joseph, Missouri. The Sioux City, Iowa, streamflowgaging station provides a view of the flow regime for discharges that are representative of the upstream 300 km of the 

LMOR. Flooding assessments were performed at Nebraska 

City, Nebraska, and St. Joseph, Missouri, because these were 

areas identified by stakeholders as sensitive to flooding.

Alternative flow-regime scenarios for this analysis were 

developed through collaborative discussion within the plenary 

group. Conceptual hydrographs developed through discussions were coded into reservoir release rules for the DRM 

(U.S. Army Corps of Engineers, 2005). Different sub-groups 

within the plenary group developed conceptual hydrographs 

that varied according to ecological and social values held by 

the group (table 1). In addition to the general shape of the 

conceptual hydrograph, rules are required to address varying 

hydroclimatic conditions from year to year. Variable hydroclimatic conditions are addressed with storage precludes and 

flood-control constraints. Storage precludes account for low 

storage in the reservoirs during drought by limiting springpulse releases from Gavins Point Dam. Precludes stipulate 

an amount of storage that is necessary before a pulse can be 

released, and may stipulate a prorationing of flow for the 

pulse based on storage on certain dates (U.S. Army Corps of 

Engineers, 2006b). The rules also account for high-flow years 

by using flood-control constraints. Flood-control constraints 

limit releases of pulses during wet climatic conditions by 

setting maximum target flows downstream in the mainstem. 

Flood-control constraints are the flows that turn off upstream 

releases, so they must be relaxed (increased or lifted) in many 

years to allow pulses to occur. Flow-regime scenarios, storage 

precludes, and flood-control constraints are listed in table 2.

Visualization of Model Results

DRM output data for reference and alternative flow 

regimes were analyzed to provide a graphical understanding 

of similarities and differences among scenarios. The method 

involved calculating duration hydrographs to show annual 

and inter-annual variability of discharge on a single graph 

(Jacobson and Heuser, 2001). Inter-annual variability is shown 

as the band of daily discharges from 25 percent exceedance to 

75 percent exceedance as modeled by the DRM. To provide a 

graphical comparison with reference flow regimes, duration 

hydrographs of alternatives were superimposed graphically on 

the ROR and NWCP duration hydrographs (figs. 2–9). 

Extracting Flow Pulses

The main analysis consisted of extracting flow pulses 

from the DRM output to compare relative performance among 

design alternatives and to compare to the reference flow 

regimes. The approach used is similar to the Index of Hydrologic Alteration (IHA) method (Richter and others, 1996; 

The Nature Conservancy, 2005) in which environmental flow 

components (EFCs) are defined as ecologically meaningful 

parameters of the flow regime. The concept of EFCs is used 

in this analysis, although the complexity of the Missouri River 

hydrograph and the design task required customized computer 

code to extract information on flow pulses.

The process employs a two-step approach in which the 

statistical properties of the population of all possible pulses 

in the flow regime were subsequently used to parameterize 

extraction of a subset of pulses thought to be ecologically 

significant. This method serves to scale the size of extracted 

pulses by inherent scale of pulses in the flow regime. The procedure was automated by Perl scripts (Practical Extraction and 

Report Language, ActiveState Corporation, Vancouver, British 

Columbia). The basic steps are given in the following list:

1. Develop an unfiltered pulse dataset (UPD) from the 

ROR flow regime at Sioux City, Iowa, by identifying 

each rising, falling, flat, and peak component of the 

hydrograph time series to isolate all pulses regardless of duration. 

•	 Beginnings and endings of all pulses were 

identified as changes in slope from decreasing to 

increasing.

•	 Peaks were identified as points or parts of the time 

series in which increasing discharge was followed 

by decreasing discharge.

•	 Because hydrographs of regulated rivers are prone 

to plateau periods of no measured change, a criterion was needed to assign a plateau to peaks or 

flats. Seven days was used as a maximum plateau 

to be identified as a peak.

•	 Each pulse in the UPD was attributed with start 

date, start discharge, peak date, peak discharge, 

end date, and end discharge. 

2. Calculate simple EFCs for each of the UPD pulses 

(table 2.).

3. Tabulate quantiles of the UPD pulses.

4. Iteratively test various quantiles for their utility as 

parameters for extracting subsets of pulses of the 

UPD, and for combining small pulses into dominant, larger pulses. This is a subjective calibration 

step in which pulses are eliminated, combined, and 

extracted depending on their EFC’s relative to quantiles of the UPD EFCs. 
4 Analysis of Pulsed Flow Modification Alternatives, Lower Missouri River, 2005 Table 1. Selected flow-regime alternative design parameters, indicators of ecological benefits, and indicators of social-economic costs. [m3/s, cubic meters per second; km3, cubic kilometers; FCC, flood-control constraint; >, greater than] Alternative parameters Pulse magnitude, Gavins Point Dam release, m3/s Preclude for pulse, system storage, km3 Relaxation of flood-control constraints, additional m3/s Alternative Early Late All Pulse Early Late ROR Run of the river NWCP Current water-control plan 0 0 RF2500 25th Percentile natural flow regime—full lift FCC 510 680 38 510 680 RF250F3 25th Percentile natural flow regime—partial lift FCC 510 680 38 280 450 HMU000 Multiple use, full lift FCC 480 570 38 480 570 HMU0F3 Multiple use, partial lift FCC 480 570 38 260 340 HMU0F0 Multiple use, no lift FCC 480 570 38 0 0 HMU0001 Multiple use, partiallLift FCC 480 570 38 260 340 HMU403 Multiple use, partial lift FCC 480 570 49.3 260 340 HMU493 Multiple use, partial lift FCC 480 570 60.4 260 340 SEC000 Socio-economic 480 570 38 260 450 Indicators of ecological benefits Indicators of social-econcomic costs Realized pulse rising peak at 

Sioux City, Iowa, 

median, m3/s

Realized pulse 

duration at Sioux 

City, Iowa, median, 

days

Annual number of 

pulses > 10% of 

reference, realized 

at Sioux City, Iowa

Design volume of spring 

pulse, km3

Minimum system 

storage during 

1930's, km3

Median days exceeding flood 

levels for agricultural land, 

March–April and May–June, 

Nebrasksa City, Nebraska

75th percentile, 

days > flood 

stage,

April–June, St. 

Joseph,

Missouri

Scenario Early Late Early Late Early Late Early Late Total Early Late All Pulses

ROR 1310 1360 50 50 1.23 1.53 NA 33 78 44.5

NWCP 290 240 20 21.5 0.6 0.34 0.18 0.33 0.51 32.8 7.1 14.2 6.0

RF2500 450 580 20 31 0.94 1.02 0.28 0.91 1.19 31.6 13.7 29.5 9.0

RF250F3 450 530 20 31 0.95 0.99 0.28 0.91 1.19 31.6 13.8 29.2 9.0

HMU000 410 480 15 28 0.71 0.92 0.18 0.33 0.51 32.5 13.9 30.1 9.0

HMU0F3 450 530 20 31 0.67 0.75 0.18 0.33 0.51 32.7 13.8 29.8 9.0

HMU0F0 300 330 18 30 0.53 0.56 0.18 0.33 0.51 33.3 13.4 26.7 9.0

HMU0001 450 530 20 31 0.67 0.75 0.18 0.33 0.51 32.7 13.8 29.8 9.0

HMU403 350 430 12 28 0.67 0.75 0.18 0.33 0.51 32.9 13.9 29.8 9.0

HMU493 360 360 16 28 0.66 0.75 0.18 0.33 0.51 33.2 13.9 29.6 9.0

SEC000 420 510 16 27 0.78 0.95 0.16 0.33 0.49 32.8 14.0 28.4 9.0

1HMU000 is repeated to show sequence of rising preludes with full lift of flood-control constraints.

Shape
Results 5

5. Once calibrated from the ROR flow regime, similar 

parameter values were used on all flow scenarios. 

Extraction of filtered pulses was based on:

•	 A primary criterion required candidate pulse peaks 

to equal or exceed the median discharge.

•	 EFCs were calculated for pulses that met this first 

criterion, and tested against a second criterion:

a. The duration must equal or exceed the median 

duration of the UPD and, 

b. Either the relative rise or the relative fall must 

exceed the 75th percentile of those variables from 

the UPD.

•	 If the pulse failed to meet the second criterion, it was 

combined with the next pulse, and retested against 

the second criterion.

•	 The next pulse in the time series was combined with 

any pulse meeting the second criterion if the relative 

rise to the next pulse peak was less than or equal to 

the 75th percentile of relative rise in the UPD.

6. New EFCs were calculated from redefined starts, 

peaks, and ends of the filtered pulses, and tabulated.

7. All discharge values in the time series were then 

reclassified as pulses or non pulses.

The design process on LMOR also needed to address the 

bimodal nature of the natural flow regime (for example, fig. 

2). Discrete date windows for the early and late spring pulses 

were defined based on the long-term record of the ROR flow 

regime. The early pulse was defined as having the peak date 

between March 1 and April 30. The later pulse was similarly 

defined as having the peak date between May 1 and July 31. 

The pulses may start or end beyond these dates, but the pulses 

are identified from the record as those with peaks that occur 

within these date windows.

Graphical and Statistical Analysis of Pulsed 

Flow Modification Alternatives

Statistical parameters of pulse peak dates, peak discharges, relative rising peak discharges, durations, and rates of 

rise and fall were extracted from all 11 flow-regime scenarios 

(table 2). The early and late peaks were analyzed separately. 

Non-parametric, Kolmogorov-Smirnov goodness-of-fit 

statistics(Systat Software, 2006) were used to test differences 

between cumulative distribution functions of EFC’s of alternative flow regime scenarios to EFC’s of the reference flow 

regime and to each other (tables 3–9). These comparisons indicate how distributions of ecological indicators vary by flow 

design and within the context of 100 years of hydroclimatic 

variability. Flow regimes that are determined to be significantly different by this test are not necessarily ecologically 

different because the Kolmogorov-Smirnov test assesses only 

differences in the distributions, not the functions of specific 

parts of the distributions.

Results

Results of the graphical comparisons of the interquartile 

ranges of alternative flow regimes to the ROR and NWCP 

flow regimes (figs. 2–9) indicate subtle differences among the 

alternatives. Visually, minimal difference is evident between 

R25000 and R250F3, although flood-control constraints were 

completely relaxed for R25000, and only partially relaxed for 

R250F3 (figs. 2, 3). Similarly, minimal difference is evident 

visually between HMU000 and HMU0F3 (figs. 4, 5). A 

substantial difference is evident, however, in HMU0F0, an 

alternative for which there was no relaxing of flood-control 

constraints for flow pulses (fig. 6). 

The series HMU000, HMU403, and HMU493 indicate 

the effect of increasing system storage precludes on when flow 

pulses can be released (table 3, figs. 4, 7, 8). Visually, there 

is minimal difference among these alternatives. The SEC000 

alternative has a more prominent early pulse than the HMU 

series (fig. 9). The late pulse of SEC000 appears similar to that 

of the RF series.

The Kolmogorov-Smirnov tests (tables 3–10) assess 

whether or not two samples come from the same distribution 

by comparing their cumulative distribution functions (Systat 

Software, 2006). Low p-values indicate low probability that 

two samples came from the same distribution. 

Distributions of early-pulse relative rising peak magnitudes vary little among alternative design flow regimes, but 

all designs are significantly different from the ROR (table 3). 

The NWCP does not differ significantly from the HMU series. 

Table 2. Simple environmental flow components used in flowregime analysis

[m3/s, cubic meters per second; m3/s/d, cubic meters per second per day]

Environmental flow 

component Calculation Units

Duration (End date) - (Start date) Days

Relative Rising Peak (Peak discharge) - (Start 

discharge)

m3/s

Rate of Rise (Relative Rising Peak)/((Peak 

date) - (End date))

m3/s/d

Relative Falling Peak (Peak discharge) - (Start 

discharge)

m3/s

Rate of Fall (Relative Rising Peak)/((Peak 

date) - (End date))

m3/s/d

Relative Peak Greater of Relative Rising 

Peak and Relative Falling 

Peak

m3/s
6 Analysis of Pulsed Flow Modification Alternatives, Lower Missouri River, 2005

1,200

1,800

2,400

3,000

3,600

JAN 1 MAR 1 MAY 1 JULY 1 SEPT 1 NOV 1

R25000

0

600

DISCHARGE, IN CUBIC METERS PER SECOND

Run-of-the-river

reference

New water-control plan

reference

1,200

1,800

2,400

3,000

3,600

JAN 1 MAR 1 MAY 1 JULY 1 SEPT 1 NOV 1

0

600

DISCHARGE, IN CUBIC METERS PER SECOND

R250F3

Run-of-the-river

reference

New water-control plan

reference

Figure 2. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile range of daily discharge 

exceedances for the run-of-the-river reference, new water-control plan reference, and the R25000 alternative, 

modeled for historical conditions 1898–1997.

Figure 3. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile range of daily discharge 

exceedances for the run-of-the-river reference, new water-control plan reference, and the R250F3 alternative, 

modeled for historical conditions 1898–1997.
Results 7

1,200

1,800

2,400

3,000

3,600

JAN 1 MAR 1 MAY 1 JULY 1 SEPT 1 NOV 1

0

600

DISCHARGE, IN CUBIC METERS PER SECOND

HMU000

Run-of-the-river

reference

New water-control plan

reference

1,200

1,800

2,400

3,000

3,600

JAN 1 MAR 1 MAY 1 JULY 1 SEPT 1 NOV 1

0

600

DISCHARGE, IN CUBIC METERS PER SECOND

HMU0F3

Run-of-the-river

reference

New water-control plan

reference

Figure 4. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile range of daily discharge 

exceedances for the run-of-the-river reference, new water-control plan reference, and the HMU000 alternative, 

modeled for historical conditions 1898–1997.

Figure 5. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile range of daily discharge 

exceedances for the run-of-the-river reference, new water-control plan reference, and the HMU0F3 alternative, 

modeled for historical conditions 1898–1997.
8 Analysis of Pulsed Flow Modification Alternatives, Lower Missouri River, 2005

1,200

1,800

2,400

3,000

3,600

JAN 1 MAR 1 MAY 1 JULY 1 SEPT 1 NOV 1

0

600

DISCHARGE, IN CUBIC METERS PER SECOND

HMU0F0

Run-of-the-river

reference

New water-control plan

reference

1,200

1,800

2,400

3,000

3,600

JAN 1 MAR 1 MAY 1 JULY 1 SEPT 1 NOV 1

0

600

DISCHARGE, IN CUBIC METERS PER SECOND

HMU403

Run-of-the-river

reference

New water-control plan

reference

Figure 7. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile range of daily discharge 

exceedances for the run-of-the-river reference, new water-control plan reference, and the HMU403 alternative, 

modeled for historical conditions 1898–1997.

Figure 6. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile range of daily discharge 

exceedances for the run-of-the-river reference, new water-control plan reference, and the HMU0F0 alternative, 

modeled for historical conditions 1898–1997.
Results 9

1,200

1,800

2,400

3,000

3,600

JAN 1 MAR 1 MAY 1 JULY 1 SEPT 1 NOV 1

0

600

DISCHARGE, IN CUBIC METERS PER SECOND

HMU493

Run-of-the-river

reference

New water-control plan

reference

1,200

1,800

2,400

3,000

3,600

JAN 1 MAR 1 MAY 1 JULY 1 SEPT 1 NOV 1

0

600

DISCHARGE, IN CUBIC METERS PER SECOND

SEC000

Run-of-the-river

reference

New water-control plan

reference

Figure 8. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile range of daily discharge 

exceedances for the run-of-the-river reference, new water-control plan reference, and the HMU493 alternative, 

modeled for historical conditions 1898–1997.

Figure 9. Duration hydrographs, Missouri River at Sioux City, Iowa, showing interquartile range of daily discharge 

exceedances for the run-of-the-river reference, new water-control plan reference, and the SEC000 alternative, 

modeled for historical conditions 1898–1997. 
10 Analysis of Pulsed Flow Modification Alternatives, Lower Missouri River, 2005

Table 3. Comparisons of early pulse magnitude distributions.

[Two sided probabilities that distributions are equal, Kolmogorov-Smirnov non-parametric test. Paired comparisons significant at the 0.05 level are shown in bold. 

Scenarios: ROR, run-of-the-river reference; NWCP, new water-control plan reference; R2500, 25th percentile of natural reference; R250F3, 25th percentile of natural 

reference with partial lift of flood-control constraints; HMU000, multiple use with full lift of flood-control constraints; HMU0F3, multiple use with partial lift of floodcontrol-constraints; HMU0F0, multiple use with no lift of flood-control constraints; HMU403, multiple use with partial lift of flood-control constraints plus 49.3 cubic 

kilometers storage preclude; HMU493, multiple use with partial lift of flood-control constraints and 60.4 cubic kilometers storage preclude; SEC000, social-economic 

scenario no lift of flood-control constraints.

Reference 

regime

Current watercontrol plan25th percentile of 

reference regime

Multiple use, increasing floodcontrol constraintsMultiple use, increasing 

storage precludes

Socialeconomic

ROR NWCP R25000 R250F3 HMU000 HMU0F3 HMU0F0 HMU403 HMU493 SEC000

ROR 1.00

NWCP 0.00 1.00

R25000 0.00 0.00 1.00

R250F3 0.00 0.00 1.00 1.00

HMU000 0.00 0.08 0.12 0.11 1.00

HMU0F3 0.00 0.64 0.02 0.02 0.40 1.00

HMU0F0 0.00 0.47 0.00 0.00 0.07 0.46 1.00

HMU403 0.00 0.70 0.02 0.02 0.30 1.00 0.51 1.00

HMU493 0.00 0.47 0.02 0.01 0.38 1.00 0.53 1.00 1.00

SEC000 0.00 0.05 0.19 0.18 1.00 0.32 0.04 0.29 0.36 1.00

Table 4. Comparisons of late pulse magnitude distributions. 

[Two sided probabilities that distributions are equal, Kolmogorov-Smirnov non-parametric test. Paired comparisons significant at the 0.05 level are shown in bold. 

Scenarios: ROR, run-of-the-river reference; NWCP, new water-control plan reference; R2500, 25th percentile of natural reference; R250F3, 25th percentile of natural 

reference with partial lift of flood-control constraints; HMU000, multiple use with full lift of flood-control constraints; HMU0F3, multiple use with partial lift of floodcontrol-constraints; HMU0F0, multiple use with no lift of flood-control constraints; HMU403, multiple use with partial lift of flood-control constraints plus 49.3 cubic 

kilometers storage preclude; HMU493, multiple use with partial lift of flood-control constraints and 60.4 cubic kilometers storage preclude; SEC000, social-economic 

scenario no lift of flood-control constraints.

Reference 

regime

Current watercontrol plan25th percentile of 

reference regime

Multiple use, increasing floodcontrol constraintsMultiple use, increasing 

storage precludes

Socialeconomic

ROR NWCP R25000 R250F3 HMU000 HMU0F3 HMU0F0 HMU403 HMU493 SEC000

ROR 1.00

NWCP 0.00 1.00

R25000 0.00 0.00 1.00

R250F3 0.00 0.00 0.07 1.00

HMU000 0.00 0.00 0.00 0.24 1.00

HMU0F3 0.00 0.00 0.00 0.01 0.44 1.00

HMU0F0 0.00 0.00 0.00 0.00 0.00 0.02 1.00

HMU403 0.00 0.00 0.00 0.01 0.48 1.00 0.03 1.00

HMU493 0.00 0.00 0.00 0.02 0.63 0.89 0.04 1.00 1.00

SEC000 0.00 0.00 0.07 0.94 0.74 0.05 0.00 0.07 0.17 1.00
Results 11

Table 5. Comparisons of early pulse duration distributions.

[Two sided probabilities that distributions are equal, Kolmogorov-Smirnov non-parametric test. Paired comparisons significant at the 0.05 level are shown in bold. 

Scenarios: ROR, run-of-the-river reference; NWCP, new water-control plan reference; R2500, 25th percentile of natural reference; R250F3, 25th percentile of natural 

reference with partial lift of flood-control constraints; HMU000, multiple use with full lift of flood-control constraints; HMU0F3, multiple use with partial lift of floodcontrol-constraints; HMU0F0, multiple use with no lift of flood-control constraints; HMU403, multiple use with partial lift of flood-control constraints plus 49.3 cubic 

kilometers storage preclude; HMU493, multiple use with partial lift of flood-control constraints and 60.4 cubic kilometers storage preclude; SEC000, social-economic 

scenario no lift of flood-control constraints.

Reference 

regime

Current watercontrol plan25th percentile of 

reference regime

Multiple use, increasing floodcontrol constraintsMultiple use, increasing 

storage precludes

Socialeconomic

ROR NWCP R25000 R250F3 HMU000 HMU0F3 HMU0F0 HMU403 HMU493 SEC000

ROR 1.00

NWCP 0.00 1.00

R25000 0.00 0.18 1.00

R250F3 0.00 0.29 1.00 1.00

HMU000 0.00 0.03 0.03 0.02 1.00

HMU0F3 0.00 0.01 0.01 0.01 1.00 1.00

HMU0F0 0.00 0.00 0.00 0.00 0.00 0.00 1.00

HMU403 0.00 0.02 0.02 0.01 1.00 1.00 0.00 1.00

HMU493 0.00 0.10 0.11 0.07 0.95 0.96 0.00 1.00 1.00

SEC000 0.00 0.18 0.12 0.06 0.99 0.59 0.00 0.75 1.00 1.00

Table 6. Comparisons of late pulse duration distributions. 

[Two sided probabilities that distributions are equal, Kolmogorov-Smirnov non-parametric test. Paired comparisons significant at the 0.05 level are shown in bold. 

Scenarios: ROR, run-of-the-river reference; NWCP, new water-control plan reference; R2500, 25th percentile of natural reference; R250F3, 25th percentile of natural 

reference with partial lift of flood-control constraints; HMU000, multiple use with full lift of flood-control constraints; HMU0F3, multiple use with partial lift of floodcontrol-constraints; HMU0F0, multiple use with no lift of flood-control constraints; HMU403, multiple use with partial lift of flood-control constraints plus 49.3 cubic 

kilometers storage preclude; HMU493, multiple use with partial lift of flood-control constraints and 60.4 cubic kilometers storage preclude; SEC000, social-economic 

scenario no lift of flood-control constraints. 

Reference 

regime

Current watercontrol plan25th percentile of 

reference regime

Multiple use, increasing floodcontrol constraintsMultiple use, increasing 

storage precludes

Socialeconomic

ROR NWCP R25000 R250F3 HMU000 HMU0F3 HMU0F0 HMU403 HMU493 SEC000

ROR 1.00

NWCP 0.00 1.00

R25000 0.00 0.00 1.00

R250F3 0.00 0.00 0.98 1.00

HMU000 0.00 0.00 0.53 0.59 1.00

HMU0F3 0.00 0.00 0.74 0.84 1.00 1.00

HMU0F0 0.00 0.00 0.55 0.60 0.47 0.55 1.00

HMU403 0.00 0.00 0.77 0.90 1.00 1.00 0.58 1.00

HMU493 0.00 0.00 0.72 0.87 0.95 1.00 0.56 1.00 1.00

SEC000 0.00 0.00 0.13 0.18 0.46 0.74 0.32 0.60 0.73 1.00
12 Analysis of Pulsed Flow Modification Alternatives, Lower Missouri River, 2005

Table 7. Comparisons of days per year low-lying agricultural lands are affected by flows, early pulse, Nebraska City, Nebraska.

[Two sided probabilities that distributions are equal, Kolmogorov-Smirnov non-parametric test. Paired comparisons significant at the 0.05 level are shown in bold. 

Scenarios: ROR, run-of-the-river reference; NWCP, new water-control plan reference; R2500, 25th percentile of natural reference; R250F3, 25th percentile of natural 

reference with partial lift of flood-control constraints; HMU000, multiple use with full lift of flood-control constraints; HMU0F3, multiple use with partial lift of floodcontrol-constraints; HMU0F0, multiple use with no lift of flood-control constraints; HMU403, multiple use with partial lift of flood-control constraints plus 49.3 cubic 

kilometers storage preclude; HMU493, multiple use with partial lift of flood-control constraints and 60.4 cubic kilometers storage preclude; SEC000, social-economic 

scenario no lift of flood-control constraints. 

Reference 

regime

Current watercontrol plan25th percentile of 

reference regime

Multiple use, increasing floodcontrol constraintsMultiple use, increasing 

storage precludes

Socialeconomic

ROR NWCP R25000 R250F3 HMU000 HMU0F3 HMU0F0 HMU403 HMU493 SEC000

ROR 1.00

NWCP 0.00 1.00

R25000 0.00 0.32 1.00

R250F3 0.00 0.41 1.00 1.00

HMU000 0.00 0.63 0.93 0.93 1.00

HMU0F3 0.00 0.74 0.98 0.98 1.00 1.00

HMU0F0 0.00 0.74 0.98 0.98 0.98 1.00 1.00

HMU403 0.00 0.74 0.98 0.98 1.00 1.00 1.00 1.00

HMU493 0.00 0.74 0.98 0.98 1.00 1.00 1.00 1.00 1.00

SEC000 0.00 0.74 0.93 0.93 1.00 1.00 1.00 1.00 1.00 1.00

Table 8. Comparisons of days per year low-lying agricultural lands are affected by flows, late pulse, Nebraska City, Nebraska.

[Two sided probabilities that distributions are equal, Kolmogorov-Smirnov non-parametric test. Paired comparisons significant at the 0.05 level are shown in bold. 

Scenarios: ROR, run-of-the-river reference; NWCP, new water-control plan reference; R2500, 25th percentile of natural reference; R250F3, 25th percentile of natural 

reference with partial lift of flood-control constraints; HMU000, multiple use with full lift of flood-control constraints; HMU0F3, multiple use with partial lift of floodcontrol-constraints; HMU0F0, multiple use with no lift of flood-control constraints; HMU403, multiple use with partial lift of flood-control constraints plus 49.3 cubic 

kilometers storage preclude; HMU493, multiple use with partial lift of flood-control constraints and 60.4 cubic kilometers storage preclude; SEC000, social-economic 

scenario no lift of flood-control constraints.

Reference 

regime

Current watercontrol plan25th percentile of 

reference regime

Multiple use, increasing floodcontrol constraintsMultiple use, increasing 

storage precludes

Socialeconomic

ROR NWCP R25000 R250F3 HMU000 HMU0F3 HMU0F0 HMU403 HMU493 SEC000

ROR 1.00

NWCP 0.00 1.00

R25000 0.00 0.00 1.00

R250F3 0.00 0.00 1.00 1.00

HMU000 0.00 0.02 0.98 0.98 1.00

HMU0F3 0.00 0.03 0.93 0.93 1.00 1.00

HMU0F0 0.00 0.74 0.03 0.05 0.19 0.32 1.00

HMU403 0.00 0.03 0.98 0.93 1.00 1.00 0.32 1.00

HMU493 0.00 0.05 0.93 0.85 1.00 1.00 0.41 1.00 1.00

SEC000 0.00 0.05 0.52 0.52 0.98 1.00 0.41 1.00 1.00 1.00
Results 13

Table 9. Comparisons of days per year flood stage is exceeded April–June, St. Joseph, Missouri.

[Two sided probabilities that distributions are equal, Kolmogorov-Smirnov non-parametric test. Paired comparisons significant at the 0.05 level are shown in bold. 

Scenarios: ROR, run-of-the-river reference; NWCP, new water-control plan reference; R2500, 25th percentile of natural reference; R250F3, 25th percentile of natural 

reference with partial lift of flood-control constraints; HMU000, multiple use with full lift of flood-control constraints; HMU0F3, multiple use with partial lift of floodcontrol-constraints; HMU0F0, multiple use with no lift of flood-control constraints; HMU403, multiple use with partial lift of flood-control constraints plus 49.3 cubic 

kilometers storage preclude; HMU493, multiple use with partial lift of flood-control constraints and 60.4 cubic kilometers storage preclude; SEC000, social-economic 

scenario no lift of flood-control constraints.

Reference 

regime

Current watercontrol plan25th percentile of 

reference regime

Multiple use, increasing floodcontrol constraintsMultiple use, increasing 

storage precludes

Socialeconomic

ROR NWCP R25000 R250F3 HMU000 HMU0F3 HMU0F0 HMU403 HMU493 SEC000

ROR 1.00

NWCP 0.00 1.00

R25000 0.00 0.93 1.00

R250F3 0.00 0.63 0.25 1.00

HMU000 0.00 1.00 1.00 0.19 1.00

HMU0F3 0.00 0.98 1.00 0.19 1.00 1.00

HMU0F0 0.00 0.98 1.00 0.19 1.00 1.00 1.00

HMU403 0.00 0.98 1.00 0.19 1.00 1.00 1.00 1.00

HMU493 0.00 0.98 1.00 0.19 1.00 1.00 1.00 1.00 1.00

SEC000 0.00 0.98 1.00 0.19 1.00 1.00 1.00 1.00 1.00 1.00

Table 10. Comparisons of minimum monthly storage levels in reservoir system.

[Two sided probabilities that distributions are equal, Kolmogorov-Smirnov non-parametric test. Paired comparisons significant at the 0.05 level are shown 

in bold. Scenarios: ROR, run-of-the-river reference; NWCP, new water-control plan reference; R2500, 25th percentile of natural reference; R250F3, 25th 

percentile of natural reference with partial lift of flood-control constraints; HMU000, multiple use with full lift of flood-control constraints; HMU0F3, multiple use with partial lift of flood-control-constraints; HMU0F0, multiple use with no lift of flood-control constraints; HMU403, multiple use with partial lift 

of flood-control constraints plus 49.3 cubic kilometers storage preclude; HMU493, multiple use with partial lift of flood-control constraints and 60.4 cubic 

kilometers storage preclude; SEC000, social-economic scenario no lift of flood-control constraints.

Current watercontrol plan25th percentile of 

reference regime

Multiple use, increasing flood-control constraintsMultiple use, increasing 

storage precludes

Socialeconomic

NWCP R25000 R250F3 HMU000 HMU0F3 HMU0F0 HMU403 HMU493 SEC000

NWCP 1.00

R25000 0.18 1.00

R250F3 0.08 1.00 1.00

HMU000 0.31 0.01 0.00 1.00

HMU0F3 0.61 0.02 0.01 1.00 1.00

HMU0F0 0.99 0.13 0.08 0.38 0.76 1.00

HMU403 0.64 0.02 0.01 1.00 1.00 0.76 1.00

HMU493 0.71 0.02 0.01 0.99 1.00 0.85 1.00 1.00

SEC000 1.00 0.12 0.07 0.50 0.79 1.00 0.85 0.88 1.00
14 Analysis of Pulsed Flow Modification Alternatives, Lower Missouri River, 2005

The late-pulse magnitudes have a similar pattern, except that 

the NWCP differs significantly from all other alternatives, and 

the R 25000 scenario is significantly different from the HMU 

series.

Early-pulse durations of the ROR differ significantly 

from all alternatives, and the NWCP and R series scenarios 

differ significantly from the HMU series (table 5). In contrast, 

late-pulse durations of the ROR and NWCP are significantly 

different from each other, but no significant differences exist 

among the other alternatives (table 6).

The ROR differs significantly from all alternatives for the 

distributions of days of flooding of low-lying agricultural land 

in the flood plain during the early pulse near Nebraska City, 

Nebraska. The alternatives, however, do not differ significantly 

among themselves (table 7). For the late pulse, many of the 

alternatives are significantly different from the NWCP, as well 

as from the ROR. There is little significant difference among 

alternatives (table 8).

Not surprisingly, the ROR distribution of days above 

flood stage at St. Joseph, Missouri, is significantly different 

from the NWCP and all alternatives (table 9). There are no 

significant differences among the NWCP and alternatives, 

probably because rare flood events are affected minimally by 

management of the mainstem reservoir system.

There are no comparisons of minimum monthly storage 

levels under the ROR because the reservoirs are modeled as 

continuously full under that scenario. The NWCP distribution 

is not significantly different from the alternatives, and only the 

R series differs significantly from some HMU series scenarios 

(table 10).

Summary

The graphical, tabular, and statistical data presented in 

this report resulted from analysis of alternative flow regime 

designs considered by the Missouri River plenary group 

during the summer of 2005. The plenary group consisted of 

managers, stakeholders, and scientists, who were charged with 

designing an alternative flow regime for the Lower Missouri 

River. The flow regime was intended to provide increased 

seasonal variability with an emphasis on spring flow pulses 

that were thought to support reproduction and survival of the 

endangered pallid sturgeon. The plenary group attempted to 

increase variation in the flow regime, while minimizing negative effects to social and economic benefits of river management. Environmental flow components (EFCs) extracted from 

the reference natural flow regime were used to design and 

assess performance of alternative flow regimes. 

This analysis is based on modeled flow releases from 

Gavins Point Dam near Yankton, South Dakota, for nine 

alternative designs and two reference scenarios; the reference 

scenarios are the run-of-the-river (ROR) and the water- control 

plan (NWCP) implemented in 2004. The alternative designs 

were developed by the plenary group with the goal of providing pulsed spring flows while retaining traditional social and 

commercial uses of the river. Flow regime time series were 

developed by the U.S. Army Corps of Engineers using the 

Missouri River daily routing model (U.S. Army Corps of 

Engineers, 1998; 2005). 

All of the alternative flow-regime designs were statistically different from the reference flow regime for environmental flow components and for measures of flooding. Most 

alternative flow-regime designs had distributions of late-pulse 

(May-June) magnitude and duration that were statistically different from the current water-control plan. Few of the alternatives were statistically different for the early-pulse (March) 

magnitude and duration. Among the alternative flow-regime 

designs, statistical differences were more common in comparisons involving alternatives that were based on the reference 

flow regime (RF series). 

References Cited

Jacobson, R.B., and Heuser, J.L., 2001, Visualization of flow 

alternatives, Lower Missouri River: U.S. Geological Survey 

Open-File Report 02–122, available online at http://www.

cerc.usgs.gov/rss/visualize/.

Richter, B.D., Baumgartner, J.V., Powell, J., and Braun, D.P., 

1996, A method for assessing hydrological alteration within 

ecosystems: Conservation Biology, v. 10, no. 4, 

p. 1,163–1,174.

Systat Software, 2006, Statistics I: Richmond, Calif., Systat 

Inc., 492 p.

The Nature Conservancy, 2005, Indicators of Hydrologic 

Alteration: Version 7, User’s Manual, 42 p.

U.S. Army Corps of Engineers, 1998, Reservoir regulation 

studies—Daily routing model studies, master water control 

manual Missouri River review and update study: U.S. Army 

Corps of Engineers, Northwest Division, v. 2A, 137 p. 

U.S. Army Corps of Engineers, 2005, Spring rise formulation 

alternatives, U.S. Army Corps of Engineers, Northwestern 

Division; accessed August 1, 2007, at http://www.nwd-mr.

usace.army.mil/mmanual/rdeis-files.html.

U.S. Army Corps of Engineers, 2006a, Missouri River Mainstem Reservoir System—Master Water Control Manual, 

Missouri River Basin: Omaha, Nebraska, Northwestern 

Division, Missouri River Basin, Water Management Division, 431 p., available at http://www.nwd-mr.usace.army.mil/

rcc/reports/mmanual/MasterManual.pdf.

U.S. Army Corps of Engineers, 2006b, Missouri River Mainstem System—2005–2006 annual operating plan: Northwestern Division, Missouri River Basin, Water Management 

Division, 89 p. 
References Cited 15

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For more information concerning this publication, contact:

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4200 New Haven Road

Columbia, MO 65201

(573) 875–5399

Or visit the Columbia Environmental Research Center Web site at:

http://www.cerc.usgs.gov
Jacobson—Analysis of Pulsed Flow Modification Alternatives, Lower Missouri River, 2005—Open-File Report 2008–1113

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