The Stanislaus River Restoration Plan Information Site
CHAPTER
5
PRIORITIZED
RESTORATION ACTIONS AND RESEARCH
This chapter presents a list of
prioritized actions intended to remedy the limiting factors and
other stressors identified in the conceptual models described
in Chapter 4.
5.1 CRITERIA FOR PRIORITIZATION:
The list of potential actions
was first prioritized according to whether research, pilot restoration
projects, or whether full-implementation restoration projects
would be recommended. The recommendation was based on the level
of scientific uncertainty presented in the conceptual models.
Then the actions were further prioritized into a high-priority
category for those thought to result in substantial benefits for
the target fish species and to be highly feasible. A medium-priority
category was assigned to those actions believed to result in a
modest amount of benefit and/or feasibility to implement. A low-category
category was assigned to those actions that may either provide
little benefit for the fish or be difficult to implement.
5.2 ADAPTIVE MANAGEMENT:
The field of river restoration
is still largely experimental and so it is important to learn
as much as possible from individual restoration efforts (Adaptive
Management Forum Scientific and Technical Panel 2002). Adaptive
management is the planning, design, implementation, and monitoring
of restoration project to address the important questions regarding
their success and longevity.
The Adaptive Management Forum
Scientific and Technical Panel (hereafter referred to as the Panel),
which consists of
- Robert E. Bilby, Ph.D., Senior
Scientist, Weyerhaeuser Company
- Thomas Dunne, Ph.D., Profession,
Donald Bren School of Environmental Science and Management, University
of California, Santa Barbara
- Michael C. Healey, Ph.D.,
Professor, Institute for Resources and Environment and Department
of Earth and Ocean Sciences, University of British Columbia
- Robert A. Mussetter, Ph.D.,
P.E., Principal Engineer, Mussetter Engineering, Inc., Fort Collins,
Colorado
- Patrick L. Redmond, M.S.,
P.E., Civil/Geotechnical Engineer and Principal, Piedmont Engineering,
Inc., Belgrade, Montana
- Michael L. Scott, Ph.D.,
Ecologist, Stream and Riparian Ecology Section, U.S. Geological
Survey, Fort Collins Science Center
defines active adaptive management
as having the following actions:
1) Think of plausible solutions
to management problems;
2) Subject these solutions to some form of structured analysis
to determine the probable responses of the system and how uncertainty
about system response effects the likelihood of success or failure;
3) Where uncertainty in system response makes it difficult to
choose among solutions, design the management intervention so
as to test among two or more alternatives;
4) Use monitoring data to reevaluate the alternatives and improve
understanding of system behavior and optimal management.
The Panel also provided the
following recommendations after reviewing restoration projects
on the Merced River:
- Scientific input is critical
prior to project design and during the initial and active states
of the design. This input established critical objectives for
the designer, guides the project to achieve the state objectives,
and ensures quantitative post-construction monitoring to determine
if the objectives have been met. Changes in design at the latter
stages of a project should be discouraged since this affects
both scheduling and cost.
- A useful model for restoration
design is that the stream will adjust to the water and sediment
supply, subject to the other physical controls. By using available
analytical tools to evaluate the hydraulic and sediment transport
conditions over the range of expected future flows, the designers
are more likely to arrive at a design that will respond to future
flows in the expected manner.
- Project objectives should
be prioritized in the event that funding becomes limiting and
only high priority objectives can be implemented.
- Performance criteria should
be established to help evaluate project effectiveness.
- Gather sufficient baseline
data on the natural history of the target species and other native
species that use the project site.
- Baseline data and the development
of analytically sound conceptual models are important for adaptive
management. Baseline data are a vital component of all projects
to identify existing conditions, establish information to use
for project design, compare pre-construction and post-construction
conditions to measure project performance and to determine ecosystem
response.
- Make a strong commitment
to the design, implementation, and analysis of the monitoring
program.
- Evaluate the physical and
biological linkages to evaluate project effectiveness.
The Panel's strategy and recommendations
for adaptive management were used in the development of the design
recommended for the high priority actions listed below.
5.3 PRIORITIZED RESEARCH AND RESTORATION
PROJECTS:
The following list of research
and restoration projects will be prioritized based on the relative
benefits to the target species or the importance of the results
expected from each project. The justification for each action,
which is a summary of the evidence cited in the conceptual model,
will be used to determine its priority level.
For the actions selected as a
high priority, hypotheses and project/study designs will be developed
to help guide future proposals.
5.3.1 Monitoring and Analysis:
Planned and Ongoing Actions:
- Estimate fall-run Chinook
salmon escapement with carcass surveys. The California Department
of Fish and Game has been conducting these surveys since the
1940s and maintaining this database in combination with a time-series
analysis of recruitment and habitat interactions is essential
to evaluating the success of restoration and management actions.
- Determine habitat use by
juvenile salmonids in various reaches of the lower Stanislaus
River. The Fisheries Foundation began conducting annual snorkeling
surveys in 2000 to determine habitat use by juvenile and adult
salmonids between Goodwin Dam and Oakdale; however, the water
is frequently too turbid to conduct snorkel surveys downstream
of Oakdale. Additional studies are needed to investigate the
downstream extent of juvenile habitat use to help guide the selection
of restoration sites and to determine the use of impacted habitats,
such as those damaged by gravel mining, versus unrestored and
enhanced habitats.
- Determine the timing and
abundance of adult steelhead and fall-run Chinook salmon entering
the lower Stanislaus River using a counting weir. S.P. Cramer
& Associates are conducting preliminary fish counts using
a portable resistance board weir installed near Riverbank in
fall 2002 and winter 2003. The California Department of Fish
and Game is conducting studies at the Hill's Ferry Barrier on
the Merced River to determine whether handling live fish to collect
length measurments and scale samples affects gamete viability.
If impacts to spawning adults are minimal, a counting weir would
help determine the accuracy of the CDFG fall-run Chinook salmon
escapement estimates based on carcass surveys, provide the first
escapement estimates for steelhead and potentially spring-run
Chinook salmon, provide information on the timing of upstream
migrations of adult salmonids, and provide the opportunity to
collect additional length measurements and scale samples for
age determination.
- Determine the timing and
abundance of juvenile steelhead and fall-run Chinook salmon migrating
in the lower Stanislaus River. S.P. Cramer & Associates have
been operating screw traps to estimate abundance and migration
timing of juvenile salmonids at Oakdale and Caswell Park since
1994. Additional funding is needed to analyze recently collected
data to assess recent trends in juvenile abundance, migration,
and survival.
- Determine the age composition
of the fall-run Chinook salmon runs in the lower Stanislaus River
using existing scale samples. This analysis is needed to estimate
recruitment of adult Chinook salmon to the Stanislaus River and
time-series analyses of recruitment estimates are needed to assess
the cumulative benefits of restoration work and new management
actions. The AFRP has funded the California Department of Fish
and Game to conduct the initial phase of this work.
- Investigate flow and water
temperature management for juvenile salmonids. The CDFG, OID,
and SSJID are jointly developing a water temperature model for
the lower Stanislaus River and New Melones and Tulloch reservoirs.
This study will include an evaluation of the influence of Old
Melones Dam on the ability to effectively manage water temperatures
of flow releases from New Melones Reservoir.
Potential Actions:
- Monitor mortality rates of
juvenile salmonids rearing in various reaches of the lower Stanislaus
River to follow-up on S.P. Cramer & Associates screw trap
data which suggest that juvenile mortality is high in the lower
half of the river (see Section 4.3.3, subsection Predation).
Predaton, contaminants, entrainment, water temperature, and dissolved
oxygen should be evaluated as potential causes of mortality.
Comparisons should be made between the areas upstream and downstream
of Oakdale and between habitats damaged by gravel mining and
enhanced or restored habitats.
- Investigate the effects of
disease organisms on juvenile salmonid survival. Disease has
been a cause of juvenile salmonid mortality in other rivers,
but nothing is known about diseases in wild fish in the lower
San Joaquin River basin (see Section 4.3.3, subsection Disease).
- Investigate erosion and sedimentation
effects on spawning habitat. Storm runoff is quite turbid downstream
of the Orange Blossom Bridge and this may result in high egg
mortality and low utilization of spawning habitat downstream
of the bridge (see Section 4.3.2). Another problem is that large
volumes of sand stored on the bottom of mined channels are mobilized
during high flows and deposited in spawning and rearing habitat
(See Section 4.3.2). Although adult salmonids remove sand and
silt from spawning gravel during redd construction, redd superimposition
in sandy habitats may result in high rates of alevin entombment
(see the introduction to Section 4.3).
- Monitor steelhead and spring-run
Chinook salmon use of spawning habitat to determine periodicity
and distribution (see Sections 4.2.2, 4.2.3, and 4.4.2).
- Record a digital video with
continuous GPS coordinates from a helicopter flown at a height
of 100 to 200 feet over the river between Goodwin Dam and the
confluence with the San Joaquin River. It would be useful for
planning purposes because it provides a high-quality, close-up
view of water flowing through the habitat as well as detailed
individual images of possible restoration and/or research sites.
Total cost of about $10,000.
- Revise and update time-series
analyses of fall-run Chinook salmon recruitment to evaluate benefits
of restoration projects and new management strategies. The purpose
of the analysis is to factor-out the influences of restoration
and management from the influences of habitat, such as Delta
flows, ocean conditions, and exports, and populations variables,
such as the number of spawners, on population recruitment (i.e.,
the number of adults that survive to either spawn or be harvested)
over time. The revision would utilize the age determinations
based on the CDFG scale analysis.
- Reduce poaching and the use
of illegal fishing methods particularly for spring-run Chinook
salmon and steelhead (see Section 4.4.2).
5.3.2 Focused Research:
Planned and Ongoing Actions:
- Investigate whether flows
and/or Delta export rates between mid-May and late-June block
passage or cause straying of adult spring-run Chinook salmon
migrating through the San Joaquin Delta. There is concern because
the South Delta Improvement Program intends to increase the capacity
and the amount of water exported at the Delta pumping facilities
of the State Water Project (see Section 4.2.1). The investigation
should be based on the assumption that passage occurs when water
temperatures are less than 65 oF and no more than 350% to 400%
of Vernalis flows are exported. This analysis should be conducted
for the Environmental Impact Report/Environmental Impact Statement
for the South Delta Improvement Program.
- Investigate whether flows
and/or Delta export rates in mid-October block passage or cause
straying of adult fall-run Chinook salmon migrating through the
San Joaquin Delta. As with adult spring-run Chinook salmon, there
is concern because the South Delta Improvement Program intends
to increase the capacity and the amount of water exported at
the Delta pumping facilities of the State Water Project (see
Section 4.3.1, subsection Adult Straying). The investigation
would be based on the assumption that passage occurs when water
temperatures are less than 65 oF and no more than 350% to 400%
of Vernalis flows are exported. This analysis should be conducted
for the Environmental Impact Report/Environmental Impact Statement
for the South Delta Improvement Program.
- Investigate whether flows
and/or Delta export rates in spring affect smolt survival between
the lower Stanislaus River and Jersey Point. As a requirement
of the San Joaquin River Agreement, the Vernalis Adaptive Management
Plan began pilot studies in spring 1998 to study the survival
of coded-wire-tagged juvenile salmon from the Merced Fish Facilities
between the lower Stanislaus River and Jersey Point when the
Head of the Old River Barrier (HORB) is installed in mid-April
to early-May. The U.S. Fish and Wildlife Service, Stockton Office,
conducts similar survival studies when the HORB cannot be installed
due to high flows. These studies do not investigate survival
rates between mid-May and late-June or the causes of mortality
in April (see Section 4.3.4, subsection Smolt Migration Through
The Delta).
- Investigate the effects of
flow releases on smolt survival in the Stanislaus River between
Knights Ferry and the confluence with the San Joaquin River.
CDFG has conducted smolt survival studies using coded-wire-tagged
fish from the Merced River Fish Facilities and S.P. Cramer &
Associates has marked naturally produced juvenile salmon to determine
survival rates relative to different levels of streamflow, water
temperature, and different reaches of the river. These studies
are expected to continue depending on the availability of study
fish (see Section 4.3.4, subsection Smolt Survival In The San
Joaquin River Tributaries).
- Investigate the effect of
adding gravel to restore spawning habitat and reduce redd superimposition
on the survival of salmonid eggs and emergence of alevins (See
Section 4.3.2). Carl Mesick Consultants will implement a one-year
study to evaluate the survival of planted eggs and the emergence
success of alevins in natural fall-run Chinook salmon redds at
sites restored in summer 1999, sites to be restored in summer
2004, and at natural, unrestored spawning habitat in the lower
Stanislaus River. Eggs will be planted both during the early
and the late spawning period to evaluate the impacts of turbidity
and redd superimposition on egg survival. This study is expected
to begin in fall 2004 immediately following construction of spawning
habitat sites at Frymire Ranch and Lovers Leap by Carl Mesick
Consultants with funding from the Anadromous Fish Restoration
Program.
Potential Actions:
- Determine the impact of predation
by native and exotic predators on juvenile salmonids in various
reaches of the lower Stanislaus River, and if possible, in the
mainstem San Joaquin River and Delta. There is conflicting evidence
whether predation from either native or exotic predator species
is a substantial source of mortality for wild, juvenile salmonids
in the San Joaquin River basin (see Section 4.3.3, subsection
Predation). Studies should determine the relative predation rates
in large captured mine pits and other areas degraded by mining
compared to those in relatively natural or restored habitats.
- Determine the effect of restoring
habitat in captured mine pits and other habitats degraded by
gravel mining on dissolved oxygen concentrations relative to
juvenile salmonid survival. Fish mortality has occurred at water
temperatures in the San Joaquin tributaries that should have
been suitable for salmonids based on laboratory studies (see
Section 4.3.3, subsection Dissolved Oxygen). Presumably, restoration
of riffle habitat in dredged habitats would increase the dissolved
oxygen concentration, and thereby, increase the ability of salmonids
to tolerate warm water temperatures. Other factors that are influenced
by water temperature, such as growth rate, disease, and predation
rates, should be investigated as part of this study.
- Investigate the benefits
of restoring floodplain habitat adjacent to spawning and rearing
habitat. Although the inundation of floodplain habitat that has
not been extensively encroached by riparian vegetation most likely
provides benefits for salmonids, including increased food availability
(see Section 4.3.3, subsection Floodplain Inundation), the deposition
of fine sediment during high flows which helps cleanse bed substrates
(see Section 4.3.2, subsection Floodplain Inundation), and maintaining
natural scour rates of spawning-sized gravel (see Section 3.3.4),
there are limited opportunities for the restoration of floodplain
habitat in the spawning and rearing reaches between Goodwin Dam
and Oakdale. Studies are needed to determine (1) whether floodplain
and riverine habitats must be restored in combination to ensure
long-term benefits are provided and (2) whether the benefit of
floodplain restoration justifies the relatively high cost of
property acquisition in the lower Stanislaus River.
- Conduct additional fry survival
studies in the lower Stanislaus River, mainstem San Joaquin River,
and San Joaquin Delta while monitoring the concentration of contaminants,
predation rates, entrainment, water temperatures, and dissolved
oxygen. Additional data are needed to assess the fate of juvenile
salmonids that migrate into the mainstem San Joaquin River and
Delta compared to the fate of those that migrate from the Stanislaus
River as smolts (see Section 4.3.4).
- Investigate the effects of
high water temperatures on egg viability, particularly for spring-run
Chinook salmon (see Section 4.2.1).
- Determine the range of suitable
water temperatures for juvenile salmonids in the lower Stanislaus
River (see Section 4.3.3, subsection Flows and Water Temperatures
and Section 4.4.3).
- Investigate entrainment rates
of juvenile salmonids at unscreened diversions in the lower Stanislaus
River and at the Banta-Carbona diversion in the San Joaquin River
(see Section 4.3.3, subsection Unscreened Diversions).
- Determine the percentage
of anadromous and resident O. mykiss in the lower Stanislaus
River (see Section 4.4).
5.3.3 Pilot Restoration Projects
Recent, Ongoing and Planned Projects:
- The Knights Ferry Gravel
Replenishment Project added 13,000 tons of gravel in summer 1998
to enhance spawning habitat at 18 riffles between Two-Mile Bar
and Oakdale. Studies indicated that spawner use was highest with
native gravel compared to gravel imported from the Tuolumne River.
Spawner use was also higher in gravel cleaned with a ¼-inch
screen compared to gravel cleaned with a 3/8-inch screen. Field
work for Phase I of the project was completed in February 2001.
Phase II will continue the monitoring of spawner use, egg incubation
conditions, and gravel movement in fall 2004. Chinook salmon
eggs will be planted in spawning sites constructed in summer
2004 (see project description below), in the Phase I sites constructed
in summer 1999, and in natural, unrestored sites in the Lovers
Leap and Frymire Ranch Reach to assess the effects of long-term
fine sediment intrusion on egg survival.
Potential Projects:
Recovery of the Spring-Run Chinook Salmon
Population:
- Construct a temporary barrier
from mid October to the end of December at Knights Ferry to isolate
spawning spring-run Chinook salmon in Goodwin Canyon from fall-run
Chinook salmon downstream of Knights Ferry. The evidence suggests
that genetic contamination with fall-run salmon and redd superimposition
from fall-run salmon may be the greatest problems blocking the
recovery of spring-run Chinook salmon in the lower Stanislaus
River (See Section 4.2.3). Although a barrier like the one used
at the Battle Creek Hatchery may be effective, it may be overly
restrictive for recreational users. A portable resistance board
weir may be effective without restricting recreational users.
- Restore passage for spring-run
at Goodwin, Tulloch, New Melones, and other upstream dams. Although
this action would provide greater benefits than the above action,
it may not be feasible to provide juvenile salmonids with a means
to survive their downstream migration through the reservoirs
and it would be very expensive.
Restoration of Spawning and Rearing Habitat
in Dredged and Armored Channels:
- Add gravel to construct/enhance
spawning and rearing habitat for steelhead, spring-run Chinook
salmon, and potentially fall-run Chinook salmon in Goodwin Canyon.
This action is expected to provide substantial benefits, particularly
for steelhead and spring-run Chinook salmon, and it is feasible
(see sections 4.2.2, 4.3.2, 4.3.3, 4.4.2). CDFG periodically
adds 1,000 to 2,000 tons of gravel to several locations about
one mile downstream from Goodwin Dam where the river is accessible
with a front-end loader. However, additional projects would be
relatively expensive because gravel is rapidly scoured from the
confined canyon and gravel would have to be placed with either
a large helicopter or hydraulic pump at most other locations.
- Add gravel to construct/enhance
spawning and rearing habitat for steelhead and fall-run Chinook
salmon between Knights Ferry and the Orange Blossom Bridge. This
action is expected to provide substantial benefits and it is
feasible and relatively inexpensive.
- Add gravel to construct/enhance
spawning and rearing habitat for fall-run Chinook salmon between
the Orange Blossom Bridge and Oakdale. This action is expected
to provide substantial benefits for rearing juveniles whereas
it is unknown whether it would benefit spawning adults because
few spawners have used this reach in recent years (see Section
4.3.2). However, it would be feasible and relatively inexpensive.
- Add gravel to construct/enhance
rearing habitat for fall-run Chinook salmon downstream of Oakdale.
There are insufficient data to assess the potential benefits
from this action. Use by juvenile salmonids of this reach has
not been determined because high turbidity makes it difficult
to observe juvenile habitat use in this reach (see Section 4.3.3).
As with the above action, it is unknown whether spawning adults
would benefit because spawner use of this reach has been low
in recent years (see Section 4.3.2)
Restoration of Spawning and Rearing Habitat
in Captured Mine Pits:
- Restore spawning and rearing
habitat in captured mine pits between Knights Ferry and the Orange
Blossom Bridge. The benefits, including reducing fine sediment
storage and increasing availability of spawning and rearing habitats
(see sections 3.3.5, 4.3.2, subsection Gravel Mining Impacts,
and 4.4.3), would be substantial and most sites are accessible
and feasible. However these projects are relatively expensive
due to the large volume of material needed to fill the pits.
- Restore spawning and rearing
habitat in captured mine pits between the Orange Blossom Bridge
and Oakdale. The benefits, including reducing fine sediment storage,
would be substantial for rearing juveniles but perhaps only modest
for spawning adults. Most sites are accessible and feasible,
but relatively expensive.
Restoration of Functional Floodplain
at Existing Flow Regime:
- Restore floodplain habitat
between Knights Ferry and the Orange Blossom Bridge to function
within the existing flow regime. The benefits, including restoring
normal rates of gravel scour from spawning habitat, trapping
fine sediment during annual high flows, improving food production
for juveniles, and providing refuge for juveniles during floods
(see sections 4.3.2, subsection Loss of Floodplain Habitat, 4.3.3,
subsection Floodplain Inundation), would probably be modest to
substantial for all three runs of salmonids. Furthermore, gravel
removed to restore floodplain habitat could be used to restore
spawning and rearing habitat. However, it is likely that floodplain
restoration is feasible only on U.S. Army Corps fee property
or where landowners are cooperative, and riparian encroachment
would have to be mechanically maintained. Most other sites are
too expensive (>$5,000 per acre) to purchase for restoration.
- Restore floodplain habitat
between the Orange Blossom Bridge and Oakdale to function within
the existing flow regime. The benefits from these projects for
adult spawners and rearing juveniles may decline in a downstream
direction since relatively few juveniles and adults currently
utilize the habitat below the Orange Blossom Bridge. However,
restoration may increase salmonid use in this reach. Drawbacks
are the same as for the upstream reach: floodplain restoration
is probably feasible only on U.S. Army Corps fee property and
riparian encroachment would have to be mechanically maintained.
- Restore floodplain habitat
downstream from Oakdale to function within the existing flow
regime. Although the benefits from projects downstream from Oakdale
may be less than those in upstream reaches, only a pilot restoration
project that compared similar restoration work between upstream
and downstream reaches could address this issue.
5.3.4 Full-Implementation Projects:
Past, Ongoing, And Planned Projects:
- The Horseshoe Road Salmon
Spawning Project was implemented by the California Department
of Fish and Game and the California Department of Water Resources
in 1994 with funds provided by the Four-Pumps Agreement. At three
sites near the Horseshoe Road Park, silty gravel was removed
from the riverbed and replaced with clean gravel imported from
the Merced River.
- The Stanislaus River Goodwin
Canyon Gravel Replenishment Project is an ongoing project managed
by the California Department of Fish and Game and the California
Department of Water Resources for which 1,000 to 2,000 tons of
Stanislaus River gravel are added to the river bed about one
mile downstream from Goodwin Dam. Gravel was added in 1997, 1998,
and 2000.
- The Mohler Riparian Acquisition
and Restoration Project was implemented by the U.S. Fish and
Wildlife Service between 1998 and 2001 with funding from the
AFRP. This project acquired 36 acres and 1,200 lineal feet of
floodplain habitat in the Stanislaus River about nine miles upstream
from the confluence with the San Joaquin River. The property
floods at flows in excess of 4,000 cfs. Restoration planning
is underway.
- Spawning and Rearing Habitat
Restoration in the Stanislaus River at Frymire Ranch and Lovers
Leap will create approximately 22 riffle-pool habitats in the
1.7-mile-long, four- to eight-foot deep, ditch-like, mined channel
about 6 miles downstream of Goodwin Dam in 2004. The AFRP has
funded Carl Mesick Consultants and a team of subconsultants to
purchase and clean on-site 13,000 cubic-yards (22,000 tons) of
gravel from adjacent landowners to restore spawning and rearing
habitat for Chinook salmon and steelhead in a dredged channel.
This project will build on the success of the Knights Ferry Gravel
Replenishment Project (KFGRP), which constructed nine well-used
riffle-pool habitats at the project site in summer 1999.
- Spawning and Rearing Habitat
Restoration in the Stanislaus River at Lovers Leap is a Four-Pumps
Agreement project that may begin simultaneously with the above
AFRP project. The Four-Pumps Mitigation Fund has allocated funding
for Carl Mesick Consultants for this project although the State
of California is conducting an extensive review of the contract.
If approved, another 12 riffle-pool habitats would be constructed
in the Lovers Leap reach in addition to those created for the
above AFRP project. About 7,000 cubic-yards (12,000 tons) of
gravel will be purchased from an adjacent landowner, cleaned
on-site, and placed in the river for this project.
Past, Ongoing, And Planned Projects:
5.4 UPDATING THE PLAN:
To Send Comments Contact Dr. Mesick
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