Yuba County Water Agency

YubaRiver Development Project

FERC Project No. 2246

Study 3.9

DRAFTINSTREAM FLOW

ABOVEUSACE’S ENGLEBRIGHT RESERVOIR

June 30March 8, 2010

[This study proposal was discussed at the 5/13 Relicensing Participants Study Proposal Development meetings. The redlined changes below were made by Licensee based on that meeting. Note that Licensee agreed to post this revised study proposal to the Relicensing Website in early June, and to hold a office meeting to discuss operations and settings of the ADCP unit. JML 5/13][At a subsequent meeting, Relicensing Participants asked that Licensee combine this study proposal with the instream flow study below Englebright. Jim Lynch (HDR|DTA) spoke with Julie Leimbach (FWN) and pointed out that Licensee was willing to begin a study in 2011 if agreement on the study was reached in 2010 and YCWA had budget, and he thought this study might be in that category but doubted that we could combine the two instream flow studies and get approval by the end of the year. He suggested keeping the two studies separate. Julie said she would get back to him after talking with other Relicensing Participants. Jim said he would hold on the effort to combine the two study proposals until he heard from Julie. Also, Jarvis Caldwell (HDR|DTA) spoke with Robert Hughes (CDFG) about scheduling a ACDP meeting, but a date has not been scheduled yet. JML 7/13]

1.0Project Nexus

Yuba County Water Agency’s (YCWA or Licensee) continued operation and maintenance (O&M) of the existing Yuba River Development Project (Project) has a potential to affect stream habitat for fish.

2.0Resource Management Goals of Agencies and Indian Tribes with Jurisdiction Over the Resource Studied

[Agencies – Section 5.11(d)(2) states that an applicant for a new license must in its proposed study “Address any known resource management goals of the agencies or Indian tribes with jurisdiction over the resource to be studied.” If each agency provides to YCWA a brief written description of their jurisdiction over the resource to be addressed in this study, YCWA will insert the brief description here/or attach it stating the description was provided by that agency. If not, prior to issuing the Pre-Application Document (PAD), YCWA will describe to the best of its knowledge and understanding the management goals of each agency that YCWA believes has jurisdiction over the resource addressed in this study. Licensee] [At 5/12 meeting, agencies said they might provide a single write-up for all study proposals that covers all agencies. Licensee said it would discus the write-up with Relicensing Participants when received, but said Licensees might add to Section 2 in some study proposals what it believed to be key information (e.g., noting USFWS ESA jurisdiction for ESA-listed fishes, and the SWRCB’s jurisdiction over water quality vis-à-vis the Basin Plan. Licensee 5/12]

3.0Study Goals and Objectives

The goalof the studyis to quantify fish habitat as a function of stream flow.

The objectives of the study include: 1) estimate the habitat index versus flow relationships(Weighted Useable Area, or WUA) using the Physical Habitat Simulation system (PHABSIM) for fish in Project-affected reaches upstream of the United States Army Corps of Engineer’s (USACE) Englebright Reservoir; and 2) use WUA relationships and the hydrologic record to develophabitat durationor time series analyses of fish habitat over time under existing (regulated) and unimpaired (un-regulated)flow scenarios.

4.0Existing Information and Need for Additional Information

Considerable information for Project-affected reaches exists that is important to conducting the study. Much of this information has been obtained or developed by Licensee and is provided in the Preliminary Information Package for the Project (YCWA 2009). The information includes but is not limited to:

  • Topographic, geologic, and hydrographic maps of the Project-affected reaches (Preliminary Information Package, Section 3.0, General Description of River Basin and Appendix D - Project Maps)
  • Hydrologic modeling and statistics for Project-affected reaches (Preliminary Information Package,Section 7.2, Water Resources and Appendix F - Hydrology)
  • Operations procedures for Project facilities (Preliminary Information Package, Section 6.0,Project Location Facilities and Operations)
  • Results of stream habitat mapping conducted by Licensee in 2009 (YCWA Stream Habitat Mapping Report, Attachment 3.9A to this study proposal).
  • Low altitude aerial video of all Project-affected reaches and facilities (Preliminary Information Package, Appendix E - Project Helicopter Video)
  • Existing information regarding the composition and distribution of fish species that occur in Project-affected reaches (Preliminary Information Package, Section 7.3, Aquatic Resources)

To achieve the study goals, information that is needed includes but is not limited to:

  • Confirmation of current and historic composition and distribution of fish species. This information will be developed as part of Licensee’s Stream Fish Populations Upstream of USACE’s Englebright Reservoir Study.
  • Habitat suitability criteria for target fish species and life stages
  • Field measurement of physical parameters required for PHABSIM modeling

5.0Study Methods and Analysis

5.1Study Area

For the purpose of this study, the study area includes the following six reaches:

  • Middle Yuba River

Our House Diversion Dam Reach. Approximately 7.5 miles of the Middle Yuba River from Our House Diversion Dam at RM 12.0 to the confluence of the Middle Yuba River and Oregon Creek at RM 4.5.

Oregon Creek Reach of the Middle Yuba River. Approximately 4.5 miles of the Middle Yuba River from the confluence of the Middle Yuba River and Oregon Creek at RM 4.5 to the confluence of the Middle Yuba River with the North Yuba River at RM 0.0.

  • Oregon Creek

Log Cabin Diversion Dam Reach. Approximately 4.1 miles of Oregon Creek from RM 4.1 to the confluence of Oregon Creek with the MiddleYubaRiver.

  • North Yuba River

New Bullards Bar Dam Reach. Approximately 2.3 miles of the North Yuba River from the New Bullards Bar Minimum Flow Release Powerhouse at RM 2.3 to the confluence of the North Yuba River with the Middle Yuba River at RM 0.0.

  • Yuba River

Middle/North Yuba River Reach. Approximately 5.8 miles of the Yuba River from the confluence of the North Yuba River with the Middle Yuba River at RM 39.7 to the New Colgate Powerhouse at RM 33.9.

New Colgate Powerhouse Reach. Approximately 1.7 miles of the YubaRiver from New Colgate Powerhouse at RM 33.9 to the normal maximum water surface elevation of USACE’s Englebright Reservoir at RM 32.2.

If YCWA proposes an addition to the Project, the study area will be expanded if necessary to include areas potentially affected by the addition.

5.2General Concepts and Procedures

The following general concepts and practices apply to the study:

  • Personal safety is the most important consideration of each fieldwork team.
  • Licensee will make a good faith effort to obtain permission to access private property where needed well in advance of entering the property.
  • Field crews may make minor variances to the FERC-approved study in the field to accommodate actual field conditions and unforeseen problems. When minor variances are made, Licensee’s field crew will follow the protocols in the FERC-approved study.
  • When Licensee becomes aware of major variances to the FERC-approved study, Licensee will issue an e-mail to the Relicensing Contact List describing the variance and reason for the variance. Licensee will contact by phone the Forest Service (if the variance is on National Forest System land), USFWS, SWRCB and CDFG to provide an opportunity for input regarding how to address the variance. Licensee will issue an e-mail to the Relicensing Contact List advising them of the resolution of the variance. Licensee will summarize in the final study report all variances and resolutions.
  • Licensee’s performance of the study does not presume that Licensee is responsible in whole or in part for measures that may arise from the study.
  • Global Positioning System (GPS) data will be collected using either a Map Grade Trimble GPS (sub-meter data collection accuracy under ideal conditions), a Recreation Grade Garmin GPS unit (3 meter data collection accuracy under ideal conditions), or similar units. GPS data will be post-processed and exported from the GPS unit into Geographic Information System (GIS) compatible file format in an appropriate coordinate system using desktop software. The resulting GIS file will then be reviewed by both field staff and Licensee’s relicensing GIS analyst. Metadata will be developed for deliverable GIS data sets.
  • Licensee will provide training to field crews to identify [agencies to develop a short suggested standard species list to be included here in each study proposal assuming Licensee agrees with the list – Licensee 4/15/10] that may reasonably be encountered coincidently during the performance of this study. Training will include instructions in diagnostic features and habitat associations of the above species. Field crews will also be provided laminate identification sheets showing the above species compared to other common species that may be encountered. All incidental observations will be reported in the appropriate Licensee report (e.g., incidental observations of special-status fish recorded during fieldwork for the Special-Status Turtles – Western Pond Turtle Study will be reported in Licensee’s Stream Fish Populations Study report). The purpose of this effort is not to conduct a focus study (no effort in addition the specific field tasks identified for the specific study) or to make all field crews experts in identifying all species, but only to opportunistically gather data during the performance of the study.
  • Field crews will be trained on and provided with materials (e.g. Quat) for decontaminating their boots, waders, and other equipment between study sites. Major concerns are amphibian chytrid fungus, and invasive invertebrates (e.g. zebra mussels, Dreissena polymorpha). This is of primary importance when moving: 1) between tributaries and mainstem reaches; 2) moving between basins (e.g. Middle Yuba River, Yuba River and North Yuba River); and 3) moving between isolated wetlands or ponds and river or stream environments.

5.3Study Methods

Licensee will use the PHABSIM method to model the response of fish habitat to flow in the study area. PHABSIM is the most widely accepted and applied fish habitat model in California and across the United States.

Physical habitat and hydraulic parameters will be measured and modeled using a combination of standard techniques of the United States Department of Interior, Fish and Wildlife Service (USFWS) methodology (Trihey and Wegner 1981;Bovee 1982, and Milhous et al. 1984); and the United States Geological Survey (Bovee 1997,Bovee et al. 1998, and Rantz 1982).

The general steps in the study (not necessarily in the order specified below) include: 1) selection of target species andlife stages; 2) determination of target species/lifestage periodicity; 3) Project-affected stream reach identification, segmentation, and consolidation; 4) study site and transect selection; 5) field data collection; 6) selection of HSC; 7) hydraulicand habitat modeling; and 8) habitat duration analysis. Each of these steps, including report preparation, is described below.

Licensee will obtain all necessary permits priot to fieldwork.

5.3.1Target Species andLife Stages

The species and life stages that will be included in PHABSIM modelingarebased on management importance and/or sensitivity to Project operations. Target species andlife stages are shown in Table5.3.1-1.

Table 5.3.1-1. Target species and life stages to be analyzed in the PHABSIM models.

Species / Life Stages / Location
Oncorhynchus mykiss
(Rainbow Trout) / Spawning
Fry
Juvenile
Adult Rearing / All PHABSIM reaches.
Mylopharodon conocephalus
(Hardhead) / Juvenile
Adult Rearing / In PHABSIM reaches where hardhead occurs
or its habitat is expected to occur.
Catostomus occidentalis
(SacramentoSucker) / Juvenile/Adult / In PHABSIM reaches where Sacramento sucker occurs
or itshabitat is expected to occur.
Ptychocheilus grandis
(Sacramento pikeminnow) / Juvenile/Adult / In PHABSIM reaches where Sacramento pikeminnow occurs
or its habitat is expected to occur.

5.3.2Target Species/Lifestage Periodicity

The period of year when the life stages of the target species life stages will be modeled in the study is an important component of the habitat duration model. Table 5.3.1-2 shows the periodicity that will be used in the study for each target species and lifestage.

Table 5.3.1-2. Periodicity of target species/lifestagesto be analyzed in the PHABSIM models.

Species / Lifestage / Jan / Feb / Mar / Apr / May / Jun / Jul / Aug / Sep / Oct / Nov / Dec
Rainbow
Spawning
Juvenile
Adult
Sacramento Sucker / Juvenile
Adult
Sacramento Pikeminnow/
Hardhead / Juvenile
Adult

5.3.3Project-affected Stream Reach Identification, Segmentation, and Consolidation

Project-affected stream reaches are delineated as described in Section 5.1, above. This delineation is based on Project flow control points and junctions of major inflows and is consistent with the delineations for the other Yuba River Development Project relicensing studies. The need for segmentation of these reaches into sub-reaches for the purposes of the PHABSIM study was evaluated by the Licensee using results fromthe habitat mapping study (Attachment 3.9A) [need to include-mb], topographic maps, low elevation aerial video, the Project hydrologic record, and tributary inflow calculations. The Licensee determined that for the purposes of the PHABSIM study,segmentation of the Project-affected reaches into sub-reaches was not warranted for the reasons discussed below.

The characteristic feature of a PHABSIM study reach is homogeneity of the channel structure and flow regime. |Generally, a ten percent or greater increase in discharge from a tributary inflow is enough to warrant a reach or sub-reach break (Bovee 1982). This general rule is most appropriate in alluvial channels rather than bedrock dominated channels. In the upper foothill and montane regions of the Projects, channel characteristics are primarily formed by bedrock control rather than fluvial processes. Bedrock channels are generally insensitive to short-term changes in sediment supply or discharge. Only a persistent decrease in discharge and/or an increase in sediment supply sufficient to convert the channel to an alluvial morphology would significantly alter fluvial bedrock channels (Montgomery and Buffington 1993). For this reason, flow accretion was not used as a dominant factor in river segmentation for this study but was evaluated as presented below in table 5.3.3-1. As table 5.3.3-1 illustrates withing the Project-affected river reaches no single tributary is likely to increase total river flow by more than 10%.

Changes in gross channel structure were evaluated next as a basis for segmentation. These included gradient, channel type, sediment supply, and other factors derived from the Initial Channel Classification report (YCWA 2009c) and the Habitat Mapping Study Report (Attachment 3.9A).

Table 5.3.3-1. Potential tributary flow contribution based on drainage area.

River / Reach Name / Named
Tributaries / Percent Contribution
(by drainage area1)
Middle Yuba River / Our House Diversion Dam Reach / Grizzley Creek / 5.32%
Nevada Creek / 0.68%
Oregon Creek Reach of the Middle Yuba River / Moonshine Creek / 2.04%
Clear Creek / 1.48%
Yellow Jacket Creek / 0.81%
Oregon Creek / Log Cabin Diversion Dam Reach / None
North Yuba River / New Bullards Bar Dam Reach / None
Yuba River / Middle/North Yuba River Reach / Sweetland Creek / 0.74%
New Colgate Powerhouse Reach / Dobbins Creek / 1.62%
1/ percent of contributing drainage to total drainage area upstream

Table 5.3.3-2 below describes the longitudinal similarities and dissimilarities in channel structure and fluvial process within the designated Project-affected reaches.

Table 5.3.3-2. Longitudinal similarities and dissimilarities in channel structure and fluvial processes

River / Reach Name / Longitudinal Similarities and Dissimilarities in Channel Structure and Fluvial Processes / Sub-reach Waranted?
Middle Yuba River / Our House Diversion Dam Reach / 100% of this 7.5 mile reach is classified as Rosgen “B” type channel with an average gradient of 1% to 3%. / No
Oregon Creek Reach / 100% of this 4.5 mile reach is classified as Rosgen “B” type channel with an average gradient of 1% to 3% / No
Oregon Creek / Log Cabin Diversion Dam Reach / Approximately 68% of this 4.1 mile reach in the vicinity of Celestial Valley is classified as Rosgen B, confined with a gradient or 1% to 3% while the remaining 32% is classified as Rosgen A, confined with a gradient of 3%-8%. / Celestial Valley Possible
North Yuba River / New Bullards Bar Dam Reach / Approximately 93% of this 2.3 mile reach is classified as “confined, Rosgen “B” type channel with a gradient of 1-3%. A short (0.2 mile section) is classified as a Rosgen “A” type channel with a gradient of 3% to 8%. / No.
Yuba River / Middle/North Yuba River Reach / 100% of this 5.8 mile reach is classified as “confined, Rosgen “B” type channel with a gradient of 1-3%. / No
New Colgate Powerhouse Reach / 100% of this 1.7 mile reach is classified as “confined, Rosgen “C” type channel with a gradient of 1%. / No

Study sites (transect or transect cluster locations) will be selected within each reach listed in Section 5.1 to represent the range of channel and habitat types in that reach as recommended in Bovee (1982).

5.3.4Meso Habitat Stratification

Meso habitat stratification isbased primarily on 2009in-river habitat mapping (channel metrics and meso habitat typing) results and the 2009 low-altitude aerial video survey (YCWA 2009a). Low-altitude video surveys were only used to type meso habitats where they were clearly visible. Aerial video was not be used to estimate channel metrics.

Video mapping was used to quantify the frequency of mesohabitats within entire PHABSIM reaches where visible. In combination, video mapping and field mapping covered 100percentof the reach length. The mapping data was used to develop a habitat unit frequency analysis for the instream flow studies. This cumulative frequency sampling approach is an extremely efficient way to inventory meso habitats over long distances (Bovee, 1997).

Habitat for an entire reach was assessed at a set interval within a range of 3-5 seconds depending on the stream width and meso-habitat length (e.g., PHABSIM reaches with short habitat units were counted at 3-second intervals, while reaches with long habitat units were counted at 5- second intervals). The video was stopped at every interval and the habitat type that was directly across the channel at the middle of the computer screen was defined and documented. A line drawn across the video screen determined the dominant habitat at that “point.” Ground-truth data for every unit that was seen in the video and mapped on the ground was used to “calibrate the eye” so that features seen in the video have a ground-based reference.