Restoration River Design for Reach 4B of the San Joaquin River from GIS and Aerial

Photographs

A Capstone Project Presented to the Faculty of Science and Environmental Policy

in the College of Science, Media Arts, and Technology

at California State University, Monterey Bay in Partial Fulfillment of the Requirements for the Degree of Bachelor of Science

By

Crystal E. Forman

May 6, 2009

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Abstract:

The San Joaquin River in the Central Valley of California is to be restored to allow

both the reintroduction of Chinook salmon and a stable water supply for water local

farmers. This study will use natural channel design methods of river restoration to find a

restoration design for a section known as Reach 4B to the restoration project. Aerial

photographs, ArcGIS v. 9.2, and Bluebeam PDR Revu were used to find the river geometries

necessary to develop a blueprint for a restored channel. The San Joaquin River watershed

was sampled for river geometries, from which three regional curves of bankfull geometry

were constructed (Estimated Bankfull width, Radius of Curvature, and Meander Length).

Sections of Reach 4B examined but not included in finally analysis. Bankfull width was

estimated from meander length. Through a regression conducted on each regional curve

data was found significant enough to design a preliminary river channel design. The

drainage area for Reach 4B was found to be 5900 km2 and this was the drainage area used

to calculate bankfull and planform geometries. It was found that bankfull width was 55m,

meander length was 360m, and radius of curvature was 120m. From DEMs it was found

that valley slope was 0.0004. Sinuosity was estimated to be 1.5 from the blueprint made

from the calculated geometries. When the blueprint was compared to the area of Reach 4B

it appeared to be similar to relic meanders. It is highly suggested that extensive field work

should be done to assess the validity of the regional curves.

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Introduction:

River Health

Very few rivers in the world have escaped alterations by anthropogenic influence.

Humans for centuries have directly altered rivers to ensure that communities have

drinking water, water for irrigation and livestock as well as water storage for dry years and

flood protection in wet years (Cech 2005, Wohl 2004). Examples of these alterations are

damming, channelization, flow diversion and rerouting, and debris removal. If these direct

alterations are done without much thought to how a river functions, they can have

devastating effects on the health of the river and the ecosystem that depends on it (Wohl

2004).

Like all geomorphic systems, rivers function within a self established, self regulated

steady state equilibrium for a certain tectonic and climatic setting (Ward & Trimble 2004,

Schumm 1977). A multitude of factors, such as discharge, sediment supply, and valley and

channel slope, shape and maintain the equilibrium of a river system (Ward & Trimble

2004). When one or more of the factors are changed due to anthropogenic alterations a

river could be thrown out of equilibrium (Rosgen 1994, Ward & Trimble 2004, Wohl 2004).

Damming, for instance, can change flow regime, discharge, sediment and bed load supply,

water temperature, water chemistry, and bank vegetation type (Cech 2005, Wohl 2004).

These kinds of disturbances to the equilibrium can lead to ecological degradation over

time. Plant and animal species within localized riparian and freshwater ecosystem have

adapted over time to the flow regime of the river they depend on. These systems depend

on the seasonal flow regime that the river has established. Probably one of the most

profound examples of this is the life cycle of salmon.

Salmon Life History

The life cycle of salmon include three interesting characteristics: anadromy, homing,

and semelparity. Andromy refers to salmon mitigation from their natal fresh water streams

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to the ocean to mature then back again to reproduce. Homing refers to the salmons’ ability

to find their natal stream for reproduction. Semelpartiy is the characteristic that applies to

the death of the salmon after it reproduces (Quinn 2005). These characteristics make

salmon an important part of freshwater ecosystems.

Salmon provide an important food source to predatory birds, fish and mammals.

Migration patterns of salmon over time have influenced the distribution and reproductions

cycles of other animals (Wilson and Halupka 1995). Predatory animals exploit all parts of

the salmon life cycle from eggs, fry and smolts on their journey to the sea, adults migration

to reproduce and the carcasses (Quinn 2005, Cederholm et al. 1999). The carcasses also

provide important nutrients, such as marine forms of nitrogen and phosphorus, for

terrestrial plants (Cederhom et al. 1999).

Over time, damming, water diversions and overfishing have caused many salmon

populations to decline significantly along the west coast of North America. Overfishing

decreases the number of adults that are able to spawn. Damming and water diversions

block salmon from their spawning grounds (Wohl 2004). The homing instinct is so strong

that salmon will die trying to reach their natal streams (Quinn 2005). Populations have

declined so much due to these influences that many of the salmon species and runs have

been put on the endangered species list (NOAA 2008).

History of the San Joaquin River and the Central Valley Chinook Salmon

The San Joaquin River (Figure 1) once hosted the southernmost Chinook salmon run

on the west coast of North America. This population has declined significantly because of

anthropogenic efforts to tame the river for agricultural use. The Central Valley Project

(CVP) is the largest State/Federal water project ever implemented; it was this project that

had the most devastating effects on the salmon population (Wagner 1995, Yoshiyama et al.

1998). The Friant Division of this project caused 60 miles of the San Joaquin River to dry up

and along with it the Upper San Joaquin River Chinook population (Wagner 1995; Figure

2).

The fate of the San Joaquin River Chinook salmon population was tied to the

proliferation of agriculture in the Central Valley along the San Joaquin River. The practice of End of Dry Channel

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irrigation started right after the Gold Rush; the ditches that once provided miners with

water became canals for agriculture. During this slice in time, about 20 years, agriculture

developed slowly. Agriculture did not begin to expand in the Central Valley until the

transcontinental railroad allowed access to the eastern markets (Taylor 1949). From 1900

to 1939 the amount of irrigated farm land increased from under a million acres to 2.75

million acre and that number would increase to 5.25 million acres by 1947 (Taylor 1949).

Even though the San Joaquin River was the life blood of the valley’s agriculture it

was also its greatest destroyer. Farmers in the valley never knew what the river had in

store for them each year. This river rarely had a ‘normal’ year of runoff. Normal runoff

year produces about 1.7 million acre feet of water. Drought years produced about 362,000

acre feet with flood years producing about 4.6 million acre feet (Rose 2000). Whether it

was drought or flood, both would spell disaster for live stock or crops.

After World War I, California experienced a drought and a severe decline in

groundwater that caused many crops to fail and water from the Sacramento Delta could not

be used because the salinity rose. These circumstances lead to the California water

regulatory agencies to come to the conclusion that a state wide water system was needed

to be able to supply farmers with water year around and help prevent flooding (Taylor

1949). Thus the States Water Plan was born and accepted into California legislation in

1933 (Taylor 1949). Eventually this plan became the Central Valley Project (CVP).

The main dam that was constructed to tame the San Joaquin River was the Friant

Dam (Figure 2). The completion of this dam and the Madera Canal was in 1944. At this

time only 10% of the water that would naturally flow down the San Joaquin River travelled

its natural course (Rose 2000). Once the Friant-Kern Canal was completed in 1948 the

natural flow amount was reduced even further. At this point 95% of the San Joaquin River’s

water was being put to irrigation use (NRDC 2007).

It was not until the late 1930’s that the California Fish and Game started to notice

there was a decline in the Chinook salmon population that utilized the Upper San Joaquin

River. A fyke netting program was conducted and it was found that there was a “significant

loss of salmon during the irrigation season”(Warner 1991). Research on the declining

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salmon population was halted due to World War II (Rose 2000). In 1946 research began

again; the spring run count of the Upper San Joaquin River population of Chinook salmon of

that year was 56,000 adults and 1947 spring run was 26,000 adults. In 1948, the majority

of water leaving the Friant Dam was sent down the newly constructed Friant Kern canal

despite the pleas of sportsman and the California Fish and Game (Rose 2000). This water

diversion caused 60 miles of the river to run dry. From 1948 to 1950 Fish and Game

workers and some local sportsman took on the task of trucking the salmon from the

confluence of the Merced River to the Outer Canal so the salmon could make it to the base

of the Friant Dam to spawn (Warner 1991). Their efforts did not save the natural resource;

it took five years to destroy an entire localized population of Chinook salmon (Warner

1991).

Fight for the Fish

In 1988 the Natural Resource Defense Council (NRDC) with a coalition of

environmentalist and other interests filed a lawsuit against the Bureau of Reclamations and

the Friant Division water users, at the time headed by Roger Patterson (Kirk Rodgers in

subsequent cases). They stated that the Friant’s long-term federal water service contracts

violated the National Environmental Protection Act (NEPA), the Endangered Species Act

(ESA), Administration Procedure Act (APA) and California Department of Fish and Game

Code § 5937 and caused loss of economic and recreational benefits by not allowing enough

water past the dam (National Resources Defense Council et al... v. Roger Patterson et al...

1992). When the long term water contracts came up for renewal in 1988 the Friant

Division of the Central Valley Project (CVP) failed to perform an Environmental Impact

Report (EIR); this was a violation of the NEPA, ESA, and APA (National Resources Defense

Council et al... v. Houston et al..., 1998). The California Department of Fish and Game Code §

5937 was violated when the Chinook salmon fishery collapsed. Code § 5937 states that the

owner and operator of any dam must allow sufficient water below that dam to keep all

fisheries, planted or natural, in ‘good condition’.

The lawsuit for the return of the Chinook salmon to the San Joaquin River took 18

years and ended in a compromise between the environmentalist and farmers. In the

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summer of 2005 Judge Lawrence Karlton told the parties that all he could do is release the

water being stored behind Friant Dam to resolve this case. The release of the water from

Friant Dam without any regulation would have caused the farmers of the Friant Division of

CVP to lose 50% of their water and with it their ability to farm. He suggested that two sides

needed to come to a compromise because he knew his judgment would lead to the

destruction of the Central Valley economy (FWUA 2006). This is when two congressional

leaders stepped in. Senator Diane Feinstein and Representative George Radanovich went

to both parties and pleaded with them to go back to the negotiation table (The San Joaquin

River Restoration Settlement Act… 2006). On September 12, 2006 both sides reached a

compromise that guaranteed that farmers would only lose 15% of their water to the river

restoration; this ensured that they could continue earning their livelihood as well as allow

for the reintroduction of a fall-run population of Chinook salmon (FWUA 2006). From this

settlement the San Joaquin River Restoration Program (SJRRP) was created.

San Joaquin River Restoration Project and Reach 4B

For the reintroduction of the Chinook salmon to be successful the river must be

restored in a way that ensures the needs of the salmon are met at certain stages of the

salmons’ life cycle (Montgomery 2004). At this stage of restoration the most important

issue is to reconnect the river so there is a fish-friendly pathway to and from the spawning

grounds. A few of the sections need little work to get the channel back to good health, but

there is one reach in particular that will take much of the SJRRP’s time and funding. That is

Reach 4B (SJRRP 2008; Figure 3).

Reach 4B is a section of the river that runs from the Sandy Slough Control Structure

downstream to the confluence of Bear Creek. It must be able to carry 4,500 cubic feet per

second (cfs) discharge (FWUA 2006). This is considered to be one of the most degraded

reaches; in its present condition is will not carry the desired rate of water flow. This

channel has not seen a constant flow of water since 1958 (Subcommittee on Water and

Power 2006). There are sections of the river that are completely clogged with tullies or the

channel banks and bed have eroded down to nothing more than a ditch that is now used by

farmers to circulate their used irrigation water for future reuse (Subcommittee on Water

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and Power 2006, Mooney 2008, personal observation). The condition of this reach has

caused the SJRRP to develop an alternative channel if it is found that the original river

channel is not feasible to be restored (SJRRP 2008).

If it is found that restoration of the original river channel is infeasible, a section of

the Eastside Flood Control Bypass will be used for fish passage (Figure 3). The section of

the Eastside Bypass that will be used runs from the Sandy Slough Control Structure to the

Mariposa Bypass (SJRRP 2008, Mooney 2008). The channel is deep with no riparian

vegetation on its banks. It can carry the amount of water necessary to facilitate salmon

migration (Subcommittee on Water and Power 2006), but without a vegetative canopy the

water temperature will vary widely which will stress the salmon (Quinn 2005).

Environmentalist and the landowners of along the river are at odds over which

alternative should be used. The environmentalists and others working with the SJRRP

want to see the original river channel restored believing this will be a more fish-friendly

alternative (Subcommittee on Water and Power 2006). Landowners want the Eastside

bypass to be used because they believe that it will be more economically feasible and they

do not want to lose any of their land. Also they do not want to be forced to make changes

that will be necessary to accommodate the endangered species that will be introduced to

their backyard (Subcommittee on Water and Power 2006). Their opposition to the original

river restoration plans is so strong they will not let officials on their land to assess the river.

Until recently the San Joaquin River Restoration Program did not have the political

or financial backing needed to persuade these farmers to comply. The regulatory agency

for SJRRP is the Bureau of Reclamation thus the program could not move forward on the

project officially until federal legislation was passed (SJRRP 2008). It took three years for

congress to pass the appropriate bills. As of March 2009 President Barak Obama just

signed a massive public lands bill, which included the San Joaquin River Restoration

Program, into law (Doyle 2009). This will finally get the restoration project underway.

River Restoration Theory

There are several theories on how a river can be successfully restored. Each river

restoration project starts with certain goals in mind that guide the project from start to

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finish as well as continued monitoring methods that will be applied once the river is

restored (Rogen 1994, Wohl 2004, Montgomery 2004). This project will rely heavily on

David Rosgen’s (1994, 2006) restoration method in order to find a restoration plan form

for the SJRRP’s Reach 4B with the goal of providing a clear passage way for Chinook Salmon

to their spawning grounds. Rosgen (1994, 2006) has developed a method that is a step by

step process to channel design for river restoration. He focuses on developing plans for a

river by using natural channels blueprints for constructed channels. This approach entails

analyzing detailed geometry of a reference reach or several reference reaches; these are

existing river segments that provide a physical model for designing a new channel.

Reference river reaches are selected because they exist in similar geologic settings and

watershed conditions presented at the restoration site. Natural channel design is an

extensive method that catalogues everything from valley morphology, river morphology,

and flow regime to human activities that will influence how the river works.

Ellen Wohl and Dorothy Morriettes (2007) and Montgomery (2008) do not believe

that natural river restoration may be not possible in some case. However, their definition

of what constitutes a natural river restoration differs from Rosgen. They believe that a

natural river restoration means that the restoration project will return a river to its

pristine, pre-human influenced conditions (Wohl 2004; Montgomery 2008). However,

Rosgen’s method uses the natural river design to create a channel that is best suited for an

area and the process does allow for modifications what that can be used to accommodate

anthropogenic influences (Rosgen 1994).

Even though Wohl and Montgomery are opponents to the method this project will

use, they do present issues that will need to be taken into consideration to ensure a

successful restoration. Wohl (2004) has studied the anthropogenic effects on river form

and function over time. Understanding how these influences have changed the river can

help in restoration plans as well as setting up monitoring protocols. Montgomery (2004)

has studied the effects geomorphology has played in the Pacific Coast salmon evolution. He

points out that a river restoration effort with salmon restoration as a goal needs to take

into consideration the life cycle of the salmon population that is being helped.

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The main focus of the project is to find the necessary river geometry to produce

blueprint of the San Joaquin River channel at Reach 4B using a natural channel design

principles. Since access to most of the river is restricted in this area, aerial photographs and

digital elevation models (DEM) will be used to find meander length, sinuosity, radius of

curvature, and drainage area for several reaches along the San Joaquin River and its

tributaries. The critical parameter of bankfull width will be calculated from meander

length and an average measurement will be estimated. Meander length, radius of curvature,

and bankfull width will be plotted, and regressed, against the drainage area of the

watershed above each reference reach. These plots and equations are called “regional

curves of bankfull geometry” (Smith et al. 2009). They will be used to estimate the channel

design parameters created for Reach 4B. Since most of Reach 4B is highly degraded and to

test the validity of the regional curves sections of Reach 4B will not be used in the final

regression analysis. The regional curves should be able to predict the geometry of Reach

4B from its drainage area even without data from this section of the channel.

Methods:

In order to find a natural river channel design for river restoration understanding

the past behavior of the channel and its natural geometry is essential. Aerial photographs,

photo reconnaissance (in areas that could be accessed), and historical accounts were used

to classify Reach 4B within the Rosgen (1994) river classification system. An analysis of

river geometries was done by the using aerial photographs, DEMs in ArcGIS 9.2 and

Bluebeam PDF Revu. Aerial photo graphs from 1998 and 2004 were obtained from the

SJRRP and DEMs were taken from the United States Geological Survey (USGS) seamless 10

meter DEM website. Sections of the San Joaquin River and its tributaries were analyzed for

river geometry. Sections were chosen for their relative geometric likeness to the whole of

the channel within the river’s natural (or anthropogenic) geomorphic breaks (Table 1).

The river geometry measurements that were taken directly from the aerial photos in

ArcGIS v. 9.2 were radius of curvature, meander width, meander length and channel and

valley length. Sinuosity and bankfull width were calculated from the measured geometries.

Slope was calculated using DEMs in ArcGIS. Arc length was calculated from central angle

measurements; central angles were measured using Bluebeam PDF Revu. Even though

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Reach 4B is not part of the analysis sections were analyzed for possible comparison to

calculated geometries.

Calculated geometries were found using hydrologic equations and standards.

Meander length was found by averaging the meander lengths of each section. Sinuosity (K)

was found by dividing channel length by valley length (K= CL/VL). Bankfull width was

estimated from meander length. Typically for meandering rivers one meander length is

equal to 10 to 14 bankfull widths (Rosgen 1994, Ward & Trimble 2004). Thus to find an

average bankfull width from this geomorphic standard, the meander length was divided by

10, 12 and 14, then the arithmetic average was taken of the three outcomes.

Once the bankfull widths were estimated a regional curve was created by finding the

drainage area of each reference reach. Drainage area was found by delineating watersheds

in ArcGIS by using of DEMs (Figure 12). When the drainage area for reach was found the

drainage area and bankfull width pairs were plotted to see if there was a statistically

significant mathematical relationship between the variables. Regional curves are

constructed to assess if the drainage area can predict the bankfull width of a river.

Microsoft Excel was used to find the power function that would explain the mathematic

relationship between drainage area and bankfull width. A regression was then conducted

to see if this relationship was significant. This was also done for radius of curvature and

meander length.

After the hydrologic geometries were assessed for the overall San Joaquin River

system the specific geometries for Reach 4B were teased out to draft a plan form for this

section of the river. The regional curves that were constructed were used to find radius of

curvature, meander length, and bankfull width. Valley slope was determined from DEMs.

Depth was found by using Manning’s equation (Manning’s roughness coefficient estimated

from photos), discharge equation (Q=VA) and the design discharge (4500 cfs; Appendix

III). All other dimensions were calculated using hydraulic standards and constants.

Results

Review of historic maps, historical written accounts and aerial photos indicate that

this section of the San Joaquin River was an anastamosing river before channelization.

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Anastamosing rivers are multichannel river with stable vegetated islands and very low

valley slope (>0.5%) (Rosgen 1994). This geometry is still visible from aerial photographs

of the section of the San Joaquin River that runs through the San Luis Wildlife Reserve

(Figure 4). Rose (2000) mentions that many of journals of frontiersman that helped settle

California mentioned that it was a maze of water ways for this area. Also, theses journals

and historical accounts state that this area once was a vast wet land habitat. This lends

support to the idea that this section of the river is anastamosing because wetland habitats

are generally associated with this type of river (Rosgen 1994; Figure 5). Even more

substantial evidence is that this area is part of the Pacific Flyway (Rose 2000).

It was found that estimated bankfull width, radius of curvature, and meander length

could be predicted by drainage area (bankfull width: y=3.625x0.316, R2 =0.484, p= 0.002;

Radius of curvature: y=2.479x0.452. R2= 0.593, p= 0.0007; meander length: y=42.69x0.316,

R2= 0.484, p= 0.002; Table 2). Since nine of the data points had similar drainage areas

(~4.99 x 103 km2 through ~ 5.94 x 103 km2), those points were averaged into one point to

avoid weighting or (leveraging) any specific part of the data set. It is common for bankfull

geometry and drainage area to be best related by a power function, so the variables are,

when plotted, a linear relationship on logarithmic axes (Figure 6-8).

When initial graphs were plotted it was revealed that the Bear Creek reaches were

outside the main cluster of data points. The data were then reanalyzed with the two points

from Bear Creek removed to assess if the data set would still produce a significant result.

Since the data set without Bear Creek was found to be significant we can conclude that

even though these two data points are not part of the main cluster of data they still fit

within the data set (bankfull width: p= 0.015; Radius of curvature: p= 0.035; meander

length: p= 0.015; Table 3; Figure 8-10)

The drainage area that was found from ArcGIS for Reach 4B was 5900 km2. From

this drainage area it was found that bankfull width was 56m, radius of curvature was

130m, and meander length was 660m. The average of meander widths was 350 m and arc

length was 250m (central angle was 120°). These measurements were then used to draft a

blueprint of a plan form for Reach 4B (Figure 14). From the blueprint sinuosity was found

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to be 1.5. To find depth, 4,500 cfs was converted into m3/s (130) then calculated using the

equation: 𝑑𝑑 = �( 𝑄𝑄∗𝑛𝑛

𝑆𝑆12∗𝑤𝑤

)35 . Slope for this equation is channel slope (0.0003) which was

derived from valley slope (0.0004) divided by sinuosity. Manning’s n was assessed from

photographs (Figure 13). Depth was found to be 2.50m which would make the width to

depth ratio 22 (Table 3).

In comparing three sections of Reach 4B it was found that the calculated dimension

were larger then what was there (Figure 27, 28; Table 4). However, it matches well with

other relic meanders in the area.

Discussion:

Results suggest that the restored section of the San Joaquin River, Reach 4B, is a C5

channel (Rosgen 1994 classification). Turning this section of the river into a single thread

meandering channel will provide a channel that will not take up as much land as a DA6

(anastamosed river) which in turn maybe more beneficial for the farmers in the area

(Rosgen 1994). The classification of 5 was assigned because the bed load will consist

mostly of sand. Moreover, C5 rivers are most commonly associated with wetland

complexes, which is fitting considering this is the environment Reach 4B was historically

and currently (Rose 2000, personal observation). Geomorphically the valley slope,

sinuosity and width to depth (w/d) ratio also suggest a C type channel as well. Rosgen

(1994) states that C type channels have a slope of < .02, a sinuosity of > 1.4 and a w/d

ratio of >12. It was found that the valley slope of the area is 0.0004, with an average

sinuosity 1.5 and a w/d of 22. When the blueprint was drafted for the area of Reach 4B it

matched closely to relic meanders present in that area (Figure 14).

In order to maintain the channel a riparian corridor needs to be established to

minimize erosion and to stabilize the banks (Rosgen 1994). Since the banks and the bed

are made mostly of mud and clay it is suggested that the riparian vegetation is given time to

grow so it can protect the new formed banks from erosion. It does not take much shear

stress to mobilize mud and clay particles and erosion of the banks could throw the river out

of equilibrium (Rosgen 1994). Also an increase amount of suspended sediment could

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inhibit the reintroduction of the Chinook salmon; high amounts of suspended sediment not

only decrease water quality it can foul the gills of the salmon and other fish species (Quinn

2005). Moreover, riparian corridor help keep water temperature stable. The canopy keeps

water from heating up too quickly during the day and losing heat too quickly at night. If

Chinook salmon were to be reintroduced without the channel being well shaded the

temperature variability would stress the salmon (Quinn 2005).

Rivers are dynamic and mobile geomorphic landforms thus ways to keep the new

channel within a confined area must be put in place. A buffer zone on either side of the

river needs to be established to give the river some room to migrate and to protect the

river from agricultural runoff. However, the river must be kept within the buffer zone to

protect agricultural land. This can be done by armoring areas that will be more susceptible

to erosion, such as the outer edge of meander loops. Armoring could be done with buried

boulders, or other barriers that are erosion resistant. The boulders would act almost like

bedrock and prevent the channel from migrating further (Rosgen 1994). This will be

necessary to protect the farmers that live along Reach 4B that do not want the channel

restored.

Even though the statistics support that the regional curves created from analyses of

aerial photographs to be used to design a blueprint for restoration of this section of the San

Joaquin River they should not completely be relied on. Extensive field work needs to be

done to validate the regional curves further. In addition to field work on the regional curves

a reference reach should be found to take hydrological dimension from for a more reliable

restoration blueprint (Rosgen 1994). This study only gives a starting point for

understanding the San Joaquin River’s watershed and approximated estimate of what the

channel for Reach 4B might look like.

Another problem with using this study for a restoration plan for Reach 4B is that all

measurements were taken from a watershed that has been heavily impacted by

anthropogenic activities. All major tributaries and the main truck of the river have been

dammed. Adding to the complexity of this river, the water in the channel past Mendota

pools comes from the Sacramento Delta. This water is delivered to the channel via the

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Delta-Mendota Canal in order to provide farmers along the river with water since the water

from Friant Dam no longer reached Mendota (Rose 2000). These and other changes could

cause immeasurable amounts of error in the data. It is likely that the watershed is still

adjusting to the human imposed barriers and diversions. Finding historical records and

photographs may add to the knowledge base needed to create a restoration plan for Reach

4B that will be successful.

It is important that the San Joaquin River Restoration Program (SJRRP) take great

care in the development of a restoration blueprint and plan not just for Reach 4B but for

the entirety of the Upper San Joaquin River. A tremendous amount of effort has gone into

ensuring the restoration of the San Joaquin River for the reintroduction of the Chinook

salmon. The compromise between environmentalist and farmer that created this

opportunity is one of the first of its kind in the Central Valley of California. This may be the

beginning of a new relationship between these two groups and the success or failure of this

project will be the foundation of their future relationship. The success in this project is

paramount to the initiation of good relations between environmentalist and farmers. Thus

the SJRRP must be diligent in designing a restoration plan that is more like to be successful.

This study may provide the initial steps in this process.

Acknowledgments:

First and for most I would like to thank my mentor Dr. Douglas Smith. Without his

wisdom, guidance and personal effort this project would have never gotten off the ground.

I would like to personally thank the San Joaquin River Restoration Program for giving me

the resource I needed to complete the project and the opportunity to join them on one of

their field trips to Reach 4B. For academic support I would like to recognize the California

State Univeristy Monterey Bay Ronald E. McNair Post Baccalaureate Program. And last but

not least I would like to acknowledge my family and friend for supporting and putting up

with me during this process.

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References:

Cech TV. 2005. Principles of Water Resources: History, Development, Management, and Policy. 2 edition. New Jersey: John Wiley & Sons Inc.

Cederholm CJ, Kunze MD, Murota T, Sibatani A. 1999 Pacific salmon carcasses. Fisheries. 26(10): 6-15.

[FWUA] Friant Water User Authority. (2006). Summary of the stipulation of settlement of Natural Resources Defense Council, et al., v. Kirk Rodgers, et al. United States District Court [Internet].[Cited 2008 April 14]. Available from: http://www.fwua.org/settlement/supplemental/docs/Summary_of_the_Settlement.pdf

Montgomery DR. November 2004. Geology, geomorphology, and the restoration ecology of salmon. GSA Today 14(11): 4-12.

Montgomery DR. (2008). Dreams of Natural Streams. Science. 319(1):291-292.

Mooney, D. 2008, July 28. C. Forman, Interviewer

National Resources Defense Council et al... v. Roger Patterson et al..., No. Civ. S-188-1658 LKK United States District Court for the Eastern District of California April 30, 1992.

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[NOAA] NOAA’s National Marine Fisheries Service Southwest Region Office. (February 20, 2008). Recovery of salmon and steelhead in California and Southern Oregan. [Interenet]. [Cited 2008 April 17]. Available from: http://swr.nmfs.noaa.gov/recovery/Chinook_CVSR.htm.

Quinn TP. 2005. The Behavior and Ecology of Pacific Salmon and Trout. 1st edition. Seattle: University of Washington Press.

Rose G. 2000. The San Joaquin a river betrayed. 2nd edition. California: Word Dancer Press.

Rosgen D. 1994. Applied River Morphology. 1st edition. Colorado: Wildland Hydrology.

Rosgen DL. 2006. River restoration using a geomorphic approach for natural channel design. In: Eighth Federal interagency Sedimentation Conference; 2006 April 2-6; Reno, NV.; p. 394-401.

[SJRRP] San Joaquin River Restoration Program. (February 2008). Temperature model sensitivity analyses set 1 &2. [Internet]. [cited 2008 21]. Available from: http://www.lib.berkeley.edu/WRCA/bayfund/pdfs/01_13SJRRestorationObjectivesIntro.pdf .

Shumm,SA. 1977. The Fluvial System. In: Ritter DF, Kochel RC, Miller JR. 2002. Process Geomorphology. 4th edition. Illinois: Waveland Press Inc.

Smith, D.P., Diehl, T., Turrini-Smith, L.A., Maas-Baldwin, J, and Croyle, Z., 2009, River restoration strategies within channelized, low-gradient landscapes of West

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Tennessee, USA; in James, A., Rathburn, S., and Whittecar, R., eds, Management and Restoration of Fluvial Systems with Broad Historical Changes and Human Impacts: Geological Sciety of America Special Paper 451., p. 000-000; doi: 10.1130/2009.245(14).

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Wohl E, Merritts DJ. 2007. What is a natural river?. In: Geography Compass: Journal compilation. New York: Blackwell Publishing Ltd; p. 871-901.

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Appendix I: Figures

Figure 1: State of California. San Joaquin River marked in dark blue. Marking exaggerated for clarity.

http://www.lib.utexas.edu/maps/us_2001/california_ref_2001.jpg

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Figure 2: Close up of the San Joaquin River. The Friant Dam is marked along with begins and end of the dry

channel. The start of the dry channel begins near Gravelly Ford and ends after Mendota Pools once the Delta-

Mendota Canal starts to feed the channel. Image from

http://www.lib.utexas.edu/maps/us_2001/california_ref_2001.jpg

Friant Dam

Gravelly Ford

Mendota-

Delta Canal

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Figure 3: Aerial Photograph of Reach 4B

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Figure 4: San Joaquin River distributaries. The interconnected channels create stable islands. The blue lines

are sloughs that are distributaries from the main channel San Joaquin River in this area.

Main Channel

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Figure 5: This is possibly how the area of Reach 4B should have looked historically. Photo by Crystal E.

Forman

Figure 6: Estimated Bankfull Width Regional Curve.

y = 3.6253x0.3169

R² = 0.4844

10.00

100.00

1000.00

1.0000E+02 1.0000E+03 1.0000E+04 1.0000E+05

Wid

th (m

)

Drainage Area (km2)

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Figure 7: Radius of Curvature Regional Curve

Figure 8: Meander Length Regional Curve

y = 2.4798x0.4526

R² = 0.5936

10

100

1000

1.0000E+02 1.0000E+03 1.0000E+04 1.0000E+05

Radi

us o

f Cur

vatu

re (m

)

Drainage Area (km2)

y = 42.69x0.3169

R² = 0.4844

100.00

1000.00

10000.00

1.0000E+02 1.0000E+03 1.0000E+04 1.0000E+05

Mea

nder

Len

gth

(m)

Drainage Area (km2)

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Figure 9: Estimated Bankfull Width Regional curve without Bear Creek data

Figure10: Radius of Curvature Regional curve without Bear Creek data

y = 0.2332x0.6241

R² = 0.5746

10.00

100.00

1000.00

1.0000E+03 1.0000E+04 1.0000E+05

Wid

th (m

)

Drainage Area (km2)

y = 0.3812x0.6623

R² = 0.4963

10

100

1000

1.0000E+03 1.0000E+04 1.0000E+05

Radi

us o

f Cur

vatu

re (m

)

Drainage Area (km2)

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Figure 11: Meander Length regional curve without Bear Creek data

Figure 12: Watersheds of the San Joaquin Watershed

y = 2.7456x0.6241

R² = 0.5746

100.00

1000.00

10000.00

1.0000E+03 1.0000E+04 1.0000E+05

Mea

nder

Len

gth

(m)

Drainage Area (km2)

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Figure 13: Part of Reach 4B.2 in the San Luis Wildlife Preserve. Photo used to asses Manning’s n. Many

riparian areas along the San Joaquin are similar to this. Not shown in photo, banks and channel are formed

from mud and silt. Photo by: Crystal Forman

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Figure 14: Rough Draft of plane form of Reach 4B with comparison to relic meanders

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Figure 15: San Joaquin River downstream from Friant Dam

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Figure 16: Bear Creek

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Figure 17: San Joaquin River upstream from the confluence of the Merced River

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Figure 18: Merced River

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Figure 19: Merced River downstream from section 5

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Figure 20: San Joaquin River below the confluence of Merced River

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Figure 21: San Joaquin River below the Sandy Slough Control Structure. Part of Reach 4B

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Figure 22: San Joaquin River below the confluence of the Delta Mendota Canal

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Figure 23: San Joaquin River below confluence of the Stanislus River

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Figure 24: San Joaquin River below the Chowchilla Bypass.

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Figure 25: San Joaquin River below the confluence of the Delta Mendota Canal downstream from section #13

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Figure 26: San Joaquin River above the Sandy Slough Control Structure

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Figure 27: San Joaquin River above the Mariposa Bypass. Reach 4B

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Figure 28: San Joaquin River below the Mariposa Bypass. Reach 4B.2

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Figure 29: San Joaquin River below the confluence of Bear Creek. Pass the end of Reach 4B

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Figure 30: San Joaquin River above the confluence Tuolumne River

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Figure 31: Tuolumne River

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Figure 32: San Joaquin River below the confluence of the Tuolumne River

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Figure 33: Stanislaus River

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Figure 34: Stanislaus River downstream from section #24

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Appendix II: Tables

Table 1: Sections of the San Joaquin River that were analyzed for geometry. Note #12 is missing because this section on closer inspection was on a section of the river that looks like there is a high rate of bank erosion. “Above” means upstream and “Below” means downstream.

Site

ID

Site Description Distance (km)

to nearest

feature

Nearest feature Figure

1 San Joaquin River Below Friant Dam

30.50 Friant Dam 15

2 Bear Creek 12.00 Confluence with SJR 16

3 Bear Creek 11.00 Confluence with SJR 16

4 Above Merced River

1.90 Confluence with the Merced River 17

5 Merced River 10.40 Confluence with SJR 18

6 Merced River 3.50 Confluence with SJR 19

7 Below Merced River

5.90 Confluence with the Merced River 20

8 Below Merced River

8.50 Confluence with the Merced River 20

9 Below Sandy Slough Control Stucture

1.40 Sandy Slough Control Sturcture 21

10 Below Delta-Mendota Canal

11.90 Chowchilla Bypass 22

11 Below Stanislaus River

1.50 Confluence with Stanislaus River 23

13 SJR Below Chaowchilla Bypass

2.70 Chowchilla Bypass 24

14 Below Delta-Mendota Canal

22.00 Chowchilla Bypass 25

15 Above Sandy Slough Control Stucture

4.40 Sandy Slough Control Sturcture 26

16 Above Sandy Slough Control Stucture

3.25 Sandy Slough Control Sturcture 26

17 Above Mariposa Bypass

3.80 Mariposia Bypass 27

18 Below Mairposa Bypass

1.30 Mariposia Bypass 28

19 Below Mairposa Bypass

4.30 Mariposia Bypass 28

20 Below Bear Creek

1.10 Confluence with Bear Creek 29

21 Above Tuolumne River

11.60 Confluence with Tuolumne River 30

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22 Tuolumne River 5.20 Confluence with SJR 31

23 Below Tuolumne River

0.15 Confluence with Tuolumne River 32

24 Stanislaus River 9.00 Confluence with SJR 33

25 Stanislaus River 5.00 Confluence with SJR 34

Table 2: Statistics for Estimated Bankfull Width, Radius of Curvature, and Meander Length. Skew of the

residuals was used to assess for normality.

Skew of

Residuals

Equation R2 p-value Figure

Estimated

Bankfull Width

-0.778 y=3.625x0.316 0.484 0.002 #6

Radius of

Curvature

-0.150 y=2.479x0.452 0.593 0.0007 #7

Meander

Length

-0.778 y=42.69x0.316 0.484 0.002 #8

Table3: Statistics for Estimated Bankfull Width, Radius of Curvature, and Meander Length without the data

from Bear Creek. Skew of Residuals was used to assess normality.

Skew of

Residuals

Equation R2 p-value Figure

Estimated

Bankfull Width

-0.826 y=0.233x0.624 0.574 0.015 #9

Radius of

Curvature

-0.272 y=0.381x0.662 0.496 0.035 #10

Meander

Length

-0.826 y=2.745x0.624 0.574 0.015 #11

Table 4: Dimensions for planform for restoration of Reach 4B

Measurement How measurement was calculated

Drainage Area (km2) 5900 ArcGIS (Figure 12)

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Bankfull Width (m) 56.0 y=3.668x0.312

Radius of Curvature (m) 130 y=2.579x0.442

Meander Length (m) 660 y=43.43x0.312

Meander Width (m) 350 Average of all sections

Sinuosity 1.5 From Blueprint

Valley Slope 0.0004 ArcGIS

Channel Slope 0.0003 Valley Slope/Sinuosity

Manning’s n 0.035 Chosen from Manning’s n Reference Table

(Figure 13)

Discharge (Q) (m3/s) 130 Converted from 4500 ft3/s as set by SJRRP

Depth (m) 2.60 𝑑𝑑 = �( 𝑄𝑄∗𝑛𝑛

𝑤𝑤∗𝑠𝑠12)35 Q=discharge,

n= Manning Coefficient, w=width, s=slop Width/depth 22 Width/depth

Arc Length (m) 250 Using Bluebeam PDF Revu to find central angle (C)

then using the equation 𝐴𝐴𝐴𝐴𝐴𝐴 𝐿𝐿𝐿𝐿𝑛𝑛𝐿𝐿𝐿𝐿ℎ = 2𝜋𝜋𝐴𝐴( 𝐶𝐶360

)

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Appendix III: Depth Calculation from Manning’s and Discharge Equation

V= velocity S= channel slope R= hydraulic radius n= manning’s coefficient

Manning’s Equation

𝑉𝑉 = 𝑆𝑆1/2∗𝑅𝑅2/3

𝑛𝑛

If we assume that the hydraulic radius (R) is equal to average depth (d) of the channel the equation becomes:

𝑉𝑉 =𝑆𝑆1/2 ∗ 𝑑𝑑2/3

𝑛𝑛

Q= Discharge V=Velocity A= Area w= width d= depth

Discharge:

Q=V*A

Since Area is equal to width * depth then the equation becomes:

Q=V*(w*d)

Since Manning’s equation equals velocity then the equation becomes:

𝑄𝑄 = �𝑆𝑆12∗𝑑𝑑

23

𝑛𝑛� ∗ (𝑤𝑤 ∗ 𝑑𝑑)

To find depth (d) the equation needs to be solved for d:

𝑄𝑄 = �𝑆𝑆

12 ∗ 𝑑𝑑

23

𝑛𝑛 � ∗ (𝑤𝑤 ∗ 𝑑𝑑) => 𝑄𝑄 = �𝑆𝑆

12 ∗ 𝑑𝑑

53 ∗ 𝑤𝑤𝑛𝑛 �

=> 𝑑𝑑5/3 =𝑄𝑄 ∗ 𝑛𝑛

𝑆𝑆12 ∗ 𝑤𝑤

=> 𝑑𝑑5 = (𝑄𝑄 ∗ 𝑛𝑛

𝑆𝑆12 ∗ 𝑤𝑤

)3 => 𝑑𝑑 = �(𝑄𝑄 ∗ 𝑛𝑛

𝑆𝑆12 ∗ 𝑤𝑤

)35