PWS_Attachment_B_-_Reach_2B_Water_Quality_Certification.pdf

Central Valley Regional Water Quality Control Board

20 November 2020

Donald E. Portz U.S. Department of the Interior, Bureau of Reclamation 2800 Cottage Way, W-1727 Sacramento, CA 95825-1898

CLEAN WATER ACT SECTION 401 WATER QUALITY CERTIFICATION AND

ORDER FOR MENDOTA POOL BYPASS AND REACH 2B IMPROVEMENTS

PROJECT, MADERA COUNTY, WDID NO. 5B20CR00092

Enclosed please find a Clean Water Act Section 401 Water Quality Certification and Order, authorized by Central Valley Regional Water Quality Control Board Executive Officer, Patrick Pulupa. This Order is issued to the United States Department of the Interior, Bureau of Reclamation (Applicant) for the Mendota Pool Bypass and Reach 2B Improvements Project (Project). Attachments A through F of the Enclosure are also part of the Order.

This Order is issued in response to an application submitted by the Applicant for proposed Project discharge to waters of the state, to ensure that the water quality standards for all waters of the state impacted by the Project are met. You may proceed with your Project according to the terms and conditions of the enclosed Order.

Please review your Order carefully to ensure that you understand all aspects of the Order. Note that this Order requires reporting and notification. Requirements for the content of the reporting and notification requirements are detailed in Attachment D, including specifications for photo and map documentation during the Project. Written reports and notifications must be submitted using the Reporting and Notification Cover Sheet located in Attachment D, which must be signed by the Permittee or an authorized representative.

These reports, notifications, and other submissions must be submitted in a searchable Portable Document Format (PDF). Documents less than 50 MB must be emailed to:

centralvalleyfresno@waterboards.ca.gov. In the subject line of the email, include the Central Valley Water Board Contact, Project name, and WDID. Documents that are 50 MB or larger must be transferred to a disk and mailed to the Central Valley Water Board Contact.

mailto:centralvalleyfresno@waterboards.ca.gov

Mendota Pool Bypass and Reach 2B Improvements Reg. Meas. ID: 428549 Place ID: 832960

If you require further assistance, please contact Brandon Salazar by phone at (559) 445-6278 or by email at Brandon.Salazar@waterboards.ca.gov. You may also contact me by phone at (559) 445-6042 or by email at Matt.Scroggins@waterboards.ca.gov.

MATTHEW S. SCROGGINS

Senior Engineer

Enclosure: 1. Clean Water Act Section 401 Water Quality Certification and Order for Mendota Pool Bypass and Reach 2B Improvements Project cc: [Via email only] (w/ enclosure):

Kathy Norton United States Army Corps of Engineers Sacramento District Headquarters Regulatory Division SPKRegulatoryMailbox@usace.army.mil

Sam Ziegler United States Environmental Protection Agency Ziegler.Sam@epa.gov

Patricia Cole United States Fish & Wildlife Service patricia_cole@fws.gov

California Department of Fish and Wildlife, Region 4 R4LSA@wildlife.ca.gov

CWA Section 401 WQC Program Division of Water Quality State Water Resources Control Board Stateboard401@waterboards.ca.gov

Andrew Minks Bureau of Reclamation aminks@usbr.gov

Steve Chedester San Joaquin River Exchange Contractors Water Authority schedester@sjrecwa.net

Central Valley Regional Water Quality Control Board

CLEAN WATER ACT SECTION 401 WATER QUALITY CERTIFICATION AND ORDER

Effective Date: 20 November 2020

Expiration Date: 20 November 2030

Program Type: Restoration

Reg. Measure: 428549 Place ID: 832960 WDID No.: 5B20CR00092 USACE No.: Individual

Project Type: Ecological Aquatic/Stream/Habitat Restoration

Project: Mendota Pool Bypass and Reach 2B Improvements (Project)

Applicant: United States Department of the Interior, Bureau of Reclamation

Applicant Contact: Donald E. Portz Program Manager 2800 Cottage Way, W-1727 Sacramento, CA 95825-1898 Phone: (916) 978-5504

Water Board Staff: Brandon Salazar Water Resource Control Engineer 1685 E Street Fresno, CA 93706 Phone: (559) 445-6278 Email: Brandon.Salazar@waterboards.ca.gov

Water Board Contact Person: If you have any questions, please call Regional Water Quality Control Board, Central Valley Region (Central Valley Water Board) Staff listed above or (559) 445-5116 and ask to speak with the Water Quality Certification Unit Supervisor.

Mendota Pool Bypass and Reach 2B Improvements Reg. Meas.ID: 428549

PID: 832960

Table of Contents

I. Order

II. Public Notice

III. Project Purpose

IV. Project Description

V. Project Location

VI. Project Impact and Receiving Waters Information

VII. Description of Direct Impacts to Waters of the State

VIII. Description of Indirect Impacts to Waters of the State- Not applicable

IX. Avoidance and Minimization

X. Compensatory Mitigation

XI. California Environmental Quality Act (CEQA)

XII. Petitions for Reconsideration

XIII. Fees Received

XIV. Conditions

XV. Water Quality Certification

Attachment A: Project Map Attachment B: Receiving Waters, Impacts, and Mitigation Information Attachment C: CEQA Findings of Facts Attachment D: Report and Notification Requirements Attachment E: Signatory Requirements Attachment F: Certification Deviation Procedures

I. Order This Clean Water Act (CWA) section 401 Water Quality Certification action and Order (Order) is issued at the request of United States Department of the Interior, Bureau of Reclamation (hereinafter Permittee) for the Project. This Order is for the purpose described in application and supplemental information submitted by the Permittee. The application was received on 11 January 2019. The application was deemed complete on 26 August 2019. Prior to receiving a complete application, Central Valley Water Board staff issued a notice of incomplete application and the Permittee responded to the request for application information on the following date(s):

Date of Notice of Incomplete Application: 14 January 2019 Date all requested information was received: 29 October 2020

II. Public Notice The Central Valley Water Board provided public notice of the application pursuant to California Code of Regulations, title 23, section 3858 from 18 October 2019 to 8 November 2019. The Central Valley Water Board did not receive any comments during the comment period.

III. Project Purpose The purpose of the Project is to implement portions of the San Joaquin River Restoration Settlement Act (Settlement). The Settlement authorizes and directs the Secretary of the Interior to implement the Settlement. Specifically, this Project is intended to implement Paragraphs 11(a)(1) and 11(a)(2) of the Settlement in Natural Resources Defense Council (NRDC), et al., v. Kirk Rodgers, et al, which are authorized in Section 10004(a)(1) of the Settlement Act.

Paragraph 11(a)(1) Creation of a bypass channel around Mendota Pool to ensure conveyance of at least 4,500 cfs from Reach 2B downstream to Reach 3. This improvement requires construction of a structure capable of directing flow down the bypass and allowing the Secretary to make deliveries of San Joaquin River water into Mendota Pool when necessary;

Paragraph 11(a)(2)

Modifications in channel capacity (incorporating new floodplain and related riparian habitat) to ensure conveyance of at least 4,500 cfs in Reach 2B between the Chowchilla Bifurcation Structure and the new Mendota Pool bypass Channel;

The Settlement specifies the need for the Project, which requires modifications to Reach 2B and construction of a bypass around Mendota Pool in support of achieving the Restoration Goal (Settlement Paragraph 2):

… a goal of this Settlement is to restore and maintain fish populations in “good condition” in the main stem of the San Joaquin River below Friant Dam to the confluence of the Merced River, including naturally-reproducing and self-sustaining populations of salmon and other fish (the “Restoration Goal”).

Therefore, the purpose of the Project is to provide increased capacity and floodplain and riparian habitat in Reach 2B and respond to the need to restore and maintain fish populations in “good condition” by providing fish passage and rearing habitat that benefit salmon and other native fish. Without the Project in Reach 2B, restoration activities would be unlikely to achieve the Settlement goals.

IV. Project Description The Project would require discharge of fill material to various wetlands and other waters of the United States including:

1. Constructing new and/or modifying existing structures associated with the Compact Bypass Channel, Mendota Pool Control Structure, Columbia Canal Facility, and Chowchilla Fish Passage Facility. Installation of these structures will permanently impact wetlands and other waters of the U.S. that occur within each structure’s footprint.

2. Constructing new set-back seepage control levees.

3. Breaching of the existing levees and subsequent grading within the San Joaquin River to restore the San Joaquin River floodplains and associated riparian habitat. Construction activities include cutting a new pilot channel upstream of the Compact Bypass Control Structure and side channels along the existing river meanders.

Project activities include construction or re-construction of the following Project components: Columbia Canal Siphon, Compact Bypass Channel, Compact Bypass Control Structure, Mendota Pool Control Structure, Reach 2B Levees, South Canal Reach 3 Levees, Road 10 ½ Bridge, Lone Willow Slough Fish Screen, Chowchilla Fish Passage Facility, Big and Little Bertha Fish Screen, utilities-gas line relocation, utilities-water lines and pipes relocation, canal regrading, and floodplain grading.

V. Project Location The Project includes all of Reach 2B and a small portion of Reach 3 of the San Joaquin River. It extends along approximately 12 miles of the San Joaquin River from the Chowchilla Bifurcation Structure to 2 miles downstream of Mendota Dam.

The Project lies within the Mendota Dam, Firebaugh, and Tranquility U.S. Geological Survey 7.5-minute topographic quadrangles. The Project area spans Fresno and Madera Counties.

Maps showing the Project location are found in Attachment A of this Order.

VI. Project Impact and Receiving Waters Information The Project is located within the jurisdiction of the Central Valley Water Board.

Receiving waters and groundwater potentially impacted by this Project are protected in accordance with the Water Quality Control Plan for the Sacramento River and San Joaquin River Basins, Fifth Edition, May 2018 (Basin Plan). The plan for the region and other plans and policies may be accessed at the State Water Resources Control Board's Plans and Policies Web page (http://www.waterboards.ca.gov/plans_policies/). The Basin Plan includes water quality standards, which consist of existing and potential beneficial uses of waters of the state, water quality objectives to protect those uses, and the state and federal antidegradation policies.

Project impact and receiving waters information can be found in Attachment B. Table 1 of Attachment B shows the receiving waters and beneficial uses of waters of the state impacted by the Project. Individual impact location and quantity is shown in Table 2 of Attachment B.

VII. Description of Direct Impacts to Waters of the State Breaching of the existing levees and grading of a pilot channel and side channels within the river will result in a direct and permanent impact to existing wetlands and other waters of the U.S., but a gradual transition in location, type, and extent of wetlands and other waters of the U.S. is expected to occur following completion of construction and active restoration. Completion of the Project is expected to result in an increase in both the function and area of waters, as described in Section X. The pilot channel is anticipated to result in gradual erosion of the Reach 2B channel upstream as the grade through Reach 2B comes into equilibrium with Reach 3.

During this time, while the topography and inundation extents and durations are adjusting, the wetlands will also be adjusting as dictated by natural processes. Some existing wetland areas not directly impacted during construction may change from one type to another, some wetland areas may convert to upland, and many upland areas will become wetlands or waters of the United States.

Table 1: Total Project Fill/Excavation Quantity for Temporary Impacts

Aquatic Resources Type Acres Stream Channel 26.33

Wetland 17.70 http://www.waterboards.ca.gov/plans_policies/

Table 2: Total Project Fill/Excavation Quantity for Permanent Physical Loss of Area Impacts

Aquatic Resources Type Acres Stream Channel 123.84

Wetland 107.90

VIII. Description of Indirect Impacts to Waters of the State- Not applicable

IX. Avoidance and Minimization Avoidance and mitigation measures will vary according to the Project component.

Component specific avoidance and mitigation measures will be submitted prior to component construction for Executive Officer approval.

X. Compensatory Mitigation Although some wetlands and other waters of the U.S. will be lost as a result of this Project, the overall improvement to the wetland and riverine system’s functions and values, the increase in total jurisdictional wetland and other waters of the U.S.

acreages, and the increase in non-jurisdictional riparian habitats are considered net benefits. Due to these net benefits, on-site restoration, increase in waters of the U.S., and no net loss of wetlands, the Project is determined to be self-mitigating.

XI. California Environmental Quality Act (CEQA) On 20 April 2017, the California State Lands Commission, as lead agency, certified an environmental impact report/environmental impact statement (EIR/EIS) (State Clearinghouse (SCH) No. 2009072044) for the Project and filed a Notice of Determination (NOD) at the SCH on 21 April 2017. Pursuant to CEQA, the Central Valley Water Board has made Findings of Facts (Findings) which support the issuance of this Order and are included in Attachment C.

XII. Petitions for Reconsideration Any person aggrieved by this action may petition the State Water Resources Control Board to reconsider this Order in accordance with California Code of Regulations, title 23, section 3867. A petition for reconsideration must be submitted in writing and received within 30 calendar days of the issuance of this Order.

XIII. Fees Received Not required for Federal project.

XIV. Conditions The Central Valley Water Board has independently reviewed the record of the Project to analyze impacts to water quality and designated beneficial uses within the watersheds of the Project. In accordance with this Order, the Permittee may proceed with the Project under the following terms and conditions:

A. Authorization Impacts to waters of the state shall not exceed quantities shown in Tables 1 and 2.

B. Reporting and Notification Requirements The following section details the reporting and notification types and timing of submittals. Requirements for the content of these reporting and notification types are detailed in Attachment D, including specifications for photo and map documentation during the Project. Written reports and notifications must be submitted using the Reporting and Notification Cover Sheet located in Attachment D, which must be signed by the Permittee or an authorized representative.

The Permittee must submit all notifications, submissions, materials, data, correspondence, and reports in a searchable Portable Document Format (PDF).

Documents less than 50 MB must be emailed to:

centralvalleyfresno@waterboards.ca.gov

In the subject line of the email, include the Central Valley Water Board Contact, Project name, and WDID No. Documents that are 50 MB or larger must be transferred to a disk and mailed to the Central Valley Water Board Contact.

1. Project Reporting

a. Monthly Reporting – Not Applicable

b. Annual Reporting: The Permittee shall submit an Annual Report each year on the 1st day of the month one year after the effective date of the Order (e.g., annual report would be due on 1 March 2021 for an Order effective on 20 February 2020). Annual reporting shall continue until the Central Valley Water Board issues a Notice of Project Complete Letter to the Permittee.

2. Project Status Notifications

a. Commencement of Construction: The Permittee shall submit a

Commencement of Construction Report at least seven (7) days prior to start of initial ground disturbance activities for each Project component identified in Attachment B, Table 2.

b. Request for Notice of Completion of Discharges Letter: The Permittee shall submit a Request for Notice of Completion of Discharges Letter following completion of construction of each Project component, including any required restoration and permittee-responsible mitigation. This request shall be submitted to the Central Valley Water Board staff within thirty (30) days following completion of each component.

c. Request for Notice of Project Complete Letter: The Permittee shall submit a Request for Notice of Project Complete Letter when construction and/or any post-construction monitoring is complete, and no further Project activities will occur. Completion of post-construction monitoring shall be determined by Central Valley Water Board staff and shall be contingent on successful attainment of restoration and mitigation performance criteria. This request shall be submitted to Central Valley Water Board staff within thirty (30) days following completion of all Project activities. Upon approval of the request, the Central Valley Water Board staff shall issue a Notice of Project Complete Letter to the Permittee which will end the post discharge monitoring period.

3. Conditional Notifications and Reports:

The following notifications and reports are required as appropriate.

a. Accidental Discharges of Hazardous Materials1

Following an accidental discharge of a reportable quantity of a hazardous material, sewage, or an unknown material, the following applies (Water Code, Section 13271):

i. As soon as (A) Permittee has knowledge of the discharge or noncompliance, (B) notification is possible, and (C) notification can be provided without substantially impeding cleanup or other emergency measures then:

• first call – 911 (to notify local response agency)

• then call – Office of Emergency Services (OES) State Warning Center at:(800) 852-7550 or (916) 845-8911

• Lastly, follow the required OES, procedures as set forth in the Office of Emergency Services’ Accidental Discharge Notification

1 "Hazardous material" means any material that, because of its quantity, concentration, or physical or chemical characteristics, poses a significant present or potential hazard to human health and safety or to the environment if released into the workplace or the environment. "Hazardous materials" include, but are not limited to, hazardous substances, hazardous waste, and any material that a handler or the administering agency has a reasonable basis for believing that it would be injurious to the health and safety of persons or harmful to the environment if released into the workplace or the environment. (Health & Safety Code, Section 25501.)

http://www.caloes.ca.gov/FireRescueSite/Documents/CalOES-Spill_Booklet_Feb2014_FINAL_BW_Acc.pdf

Web page (http://www.caloes.ca.gov/FireRescueSite/Documents/CalOES- Spill_Booklet_Feb2014_FINAL_BW_Acc.pdf)

ii. Following notification to OES, the Permittee shall notify Central Valley Water Board, as soon as practicable (ideally within 24 hours).

Notification may be delivered via written notice, email, or other verifiable means.

iii. Within five (5) working days of notification to the Central Valley Water Board, the Permittee must submit an Accidental Discharge of Hazardous Material Report.

b. Violation of Compliance with Water Quality Standards: The Permittee shall notify the Central Valley Water Board of any event causing a violation of compliance with water quality standards. Notification may be delivered via written notice, email, or other verifiable means.

i. This notification must be followed within three (3) working days by submission of a Violation of Compliance with Water Quality Standards Report.

c. In-Water Work and Diversions:

i. The Permittee shall notify the Central Valley Water Board at least forty-eight (48) hours prior to initiating work in water or stream diversions.

Notification may be delivered via written notice, email, or other verifiable means.

ii. Within three (3) working days following completion of work in water or stream diversions, an In-Water Work/Diversions Water Quality Monitoring Report must be submitted to Central Valley Water Board staff.

d. Modifications to Project Project modifications may require an amendment of this Order. The Permittee shall give advance notice to Central Valley Water Board staff if Project implementation as described in the application materials is altered in any way or by the imposition of subsequent permit conditions by any local, state or federal regulatory authority by submitting a Modifications to Project Report. The Permittee shall inform Central Valley Water Board staff of any Project modifications that will interfere with the Permittee’s compliance with this Order. Notification may be made in accordance with conditions in the certification deviation section of this Order.

e. Transfer of Property Ownership: Not applicable

f. Transfer of Long-Term BMP Maintenance: Not applicable http://www.caloes.ca.gov/FireRescueSite/Documents/CalOES-Spill_Booklet_Feb2014_FINAL_BW_Acc.pdf

C. Water Quality Monitoring

1. General:

If surface water is present, continuous visual surface water monitoring shall be conducted during active construction periods to detect accidental discharge of construction related pollutants (e.g., oil and grease, turbidity plume, or uncured concrete). The Permittee shall perform surface water sampling:

a. when performing any in-water work;

b. when in-water work is conducted during an unanticipated flow event;

c. during the entire duration of temporary surface water diversions;

d. in the event that the Project activities result in any materials reaching surface waters; or

e. when any activities result in the creation of a visible plume in surface waters.

2. Accidental Discharges/Noncompliance:

Upon occurrence of an accidental discharge of hazardous materials or a violation of compliance with a water quality standard, Central Valley Water Board staff may require water quality monitoring based on the discharge constituents and/or related water quality objectives and beneficial uses.

3. In-Water Work or Diversions:

For projects involving planned work in water or stream diversions, a water quality monitoring plan shall be submitted to Central Valley Water Board staff for acceptance at least 30 days in advance of any discharge to the affected water body. Water quality monitoring shall be conducted in accordance with the approved plan.

During planned in-water work, during in-water work during an unanticipated flow event, or during the entire duration of temporary water diversions, any discharge(s) to waters of the state shall conform to the following water quality standards:

a. Waters shall not contain oils, greases, waxes, or other materials in concentrations that cause nuisance, result in a visible film or coating on the surface of the water or on objects in the water, or otherwise adversely affect beneficial uses.

b. Activities shall not cause pH in waters of the state to be depressed below

6.5 nor raised above 8.5 in surface water.

c. Activities (i.e., controllable water quality factors) shall not cause turbidity increases in surface water to exceed:

i. where natural turbidity is less than 1 Nephelometric Turbidity Units (NTUs), controllable factors shall not cause downstream turbidity to exceed 2 NTU;

ii. where natural turbidity is between 1 and 5 NTUs, increases shall not exceed 1 NTU;

iii. where natural turbidity is between 5 and 50 NTUs, increases shall not exceed 20 percent;

iv. where natural turbidity is between 50 and 100 NTUs, increases shall not exceed 10 NTUs;

v. where natural turbidity is greater than 100 NTUs, increases shall not exceed 10 percent.

In determining compliance with the above limits, appropriate averaging periods may be applied provided that beneficial uses will be fully protected. Averaging periods may only be used with prior permission of the Central Valley Water Board Executive Officer.

Sampling during in-water work or during the entire duration of temporary water diversions shall be conducted in accordance with Table 3 sampling parameters.2 The sampling requirements in Table 3 shall be conducted upstream out of the influence of the work area, and approximately 300 feet downstream of the work area.

The sampling frequency and monitoring locations may be modified for certain projects with written approval from Central Valley Water Board staff. An In- Water Work and Diversion Water Quality Monitoring Report, as described in Attachment D, shall be submitted within two weeks of initiation of in-water construction or diversion, and every two weeks thereafter. In reporting the data, the Permittee shall arrange the data in tabular form so that the sampling locations, date, constituents, and concentrations are readily discernible. The data shall be summarized in such a manner to illustrate clearly whether the Project complies with Order requirements. The report shall include surface water sampling results, visual observations, and identification of the turbidity

2 Pollutants shall be analyzed using the analytical methods described in 40 Code of

Federal Regulations Part 136; where no methods are specified for a given pollutant, the method shall be approved by Central Valley Water Board staff. Grab samples shall be taken between the surface and mid-depth and not be collected at the same time each day to get a complete representation of variations in the receiving water. A hand-held field meter may be used, provided the meter utilizes a U.S. EPA-approved algorithm/method and is calibrated and maintained in accordance with the manufacturer’s instructions. A calibration and maintenance log for each meter used for monitoring shall be maintained onsite.

increase in the receiving water applicable to the natural turbidity conditions specified in the turbidity criteria in XIV.C.3.

If no sampling is required, the Permittee shall submit a written statement stating, “No sampling was required” within two weeks on initiation of in-water construction or diversion, and every two weeks thereafter.

Table 3: Sample Type and Frequency Requirements

Parameter Unit of Measurement

Type of Sample Minimum Frequency pH Standard Units Grab Every 4 hours

Turbidity NTU Grab Every 4 hours

Visible construction related pollutants3 Observations Visual

Inspections

Continuous throughout the construction period

4. Post-Construction: Maintenance and monitoring of the Project shall be conducted according to the Habitat Mitigation and Monitoring Plan (HMMP), December 2018. This HMMP describes the Project, including the restoration plan and proposed implementation, long-term maintenance and monitoring, success criteria, and regulatory reporting requirements.

The long-term management needs and activities necessary to maintain any on-site mitigation sites shall be resource-specific long-term maintenance activities and other general maintenance activities, such as invasive species and grazing management, clean-up and trash removal, infrastructure management (such as gate, fence, road, culvert, signage and drainage-feature repair), and other maintenance activities necessary to maintain the riparian and floodplain habitat quality. These activities shall continue for the life of the Project.

The Project includes environmental commitments, as outlined in Attachment B of the Project Environmental Impact Statement Record of Decision (ROD), applicable to construction, operation, maintenance, monitoring, and long-term management of the Mendota Pool Bypass and Reach 2B project. The Permittee will be responsible for ensuring implementation of these commitments and for monitoring and reporting requirements, as applicable.

These commitments will be implemented prior to or concurrent with construction, as applicable. In addition, the Permittee has committed to conservation measures as identified in the Biological Opinions for the Project provided by the US Fish and Wildlife Service and National Marine Fisheries

3 Visible construction-related pollutants include oil, grease, foam, fuel, petroleum products, and construction-related, excavated, organic or earthen materials.

Service. Attachments B of the Record of Decision and both Biological Opinions are available on the U.S. Bureau of Reclamation’s website at https://www.usbr.gov/mp/nepa/nepa_project_details.php?Project_ID=2940

D. Standard

1. This Order is subject to modification or revocation upon administrative or judicial review, including review and amendment pursuant to Water Code section 13330, and California Code of Regulations, Title 23, Chapter 28, article 6 commencing with sections 3867-3869, inclusive. Additionally, the Central Valley Water Board reserves the right to suspend, cancel, or modify and reissue this Order, after providing notice to the Permittee, if the Central Valley Water Board determines that: the Project fails to comply with any of the conditions of this Order; or, when necessary to implement any new or revised water quality standards and implementation plans adopted or approved pursuant to the Porter-Cologne Water Quality Control Act (Water Code, section 13000 et seq.) or federal Clean Water Act section 303 (33 U.S.C.

section 1313). For purposes of Clean Water Act section 401(d), the condition constitutes a limitation necessary to assure compliance with water quality standards and appropriate requirements of state law.

2. This Order is not intended and shall not be construed to apply to any activity involving a hydroelectric facility requiring a Federal Energy Regulatory Commission (FERC) license or an amendment to a FERC license, unless the pertinent certification application was filed pursuant to subsection 3855(b) of chapter 28, Title 23 of the California Code of Regulations, and that application specifically identified that a FERC license or amendment to a FERC license for a hydroelectric facility was being sought.

3. This Order is conditioned upon total payment of any fee required under Title 23 of the California Code of Regulations and owed by the Permittee.

4. In the event of any violation or threatened violation of the conditions of this Order, the violation or threatened violation shall be subject to any remedies, penalties, process, or sanctions as provided for under state and federal law.

For purposes of Clean Water Act, section 401(d), the applicability of any state law authorizing remedies, penalties, processes, or sanctions for the violation or threatened violation constitutes a limitation necessary to assure compliance with the water quality standards and other pertinent requirements incorporated into this Order.

E. General Compliance

1. Failure to comply with any condition of this Order shall constitute a violation of the Porter-Cologne Water Quality Control Act and the Clean Water Act. The Permittee and/or discharger may then be subject to administrative and/or civil liability pursuant to Water Code section 13385.

https://www.usbr.gov/mp/nepa/nepa_project_details.php?Project_ID=4032 http://www.restoresjr.net/downloads/?wpfb_s=biological+opinion&placeholder=Search+within+documents http://www.restoresjr.net/downloads/?wpfb_s=biological+opinion&placeholder=Search+within+documents https://www.usbr.gov/mp/nepa/nepa_project_details.php?Project_ID=2940

2. Permitted actions must not cause a violation of any applicable water quality standards, including impairment of designated beneficial uses for receiving waters as adopted in the Basin Plans by any applicable Regional Water Board or any applicable State Water Board (collectively Water Boards) water quality control plan or policy. The source of any such discharge must be eliminated as soon as practicable.

3. In response to a suspected violation of any condition of this Order, the Central Valley Water Board may require the holder of this Order to furnish, under penalty of perjury, any technical or monitoring reports the Water Boards deem appropriate, provided that the burden, including costs, of the reports shall bear a reasonable relationship to the need for the reports and the benefits to be obtained from the reports. The additional monitoring requirements ensure that permitted discharges and activities comport with any applicable effluent limitations, water quality standards, and/or other appropriate requirement of state law.

4. The Permittee must, at all times, fully comply with engineering plans, specifications, and technical reports submitted to support this Order; and all subsequent submittals required as part of this Order. The conditions within this Order and Attachments supersede conflicting provisions within Permittee submittals.

5. This Order and all of its conditions contained herein continue to have full force and effect regardless of the expiration or revocation of any federal license or permit issued for the Project. For purposes of Clean Water Act, section 401(d), this condition constitutes a limitation necessary to assure compliance with the water quality standards and other pertinent requirements of state law.

6. The Permittee shall adhere to all requirements in the habitat mitigation monitoring and reporting program (HMMP) (Mendota Pool Bypass and Reach 2B Improvements Project Habitat Mitigation and Monitoring Plan, December 2018) which is incorporated herein by reference and any additional measures as outlined in Attachment C, CEQA Findings of Fact.

7. Construction General Permit Requirement: The Permittee shall obtain coverage under the National Pollutant Discharge Elimination System (NPDES) General Permit for Storm Water Discharges Associated with Construction and Land Disturbance Activities (Order No. 2009-0009-DWQ;

NPDES No. CAS000002), as amended, for discharges to surface waters comprised of storm water associated with construction activity, including, but not limited to, demolition, clearing, grading, excavation, and other land disturbance activities of one or more acres, or where projects disturb less than one acre but are part of a larger common plan of development that in total disturbs one or more acres.

F. Administrative

1. Signatory requirements for all document submittals required by this Order are presented in Attachment E of this Order.

2. This Order does not authorize any act which results in the taking of a threatened, endangered or candidate species or any act, which is now prohibited, or becomes prohibited in the future, under either the California Endangered Species Act (Fish & Wildlife Code, sections 2050-2097) or the federal Endangered Species Act (16 U.S.C. sections 1531-1544). If a “take” will result from any act authorized under this Order held by the Permittee, the Permittee must obtain authorization for the take prior to any construction or operation of the portion of the Project that may result in a take. The Permittee is responsible for meeting all requirements of the applicable endangered species act for the Project authorized under this Order.

3. The Permittee shall grant Central Valley Water Board staff, or an authorized representative (including an authorized contractor acting as a Water Board representative), upon presentation of credentials and other documents as may be required by law, permission to:

a. Enter upon the Project or compensatory mitigation site(s) premises where a regulated facility or activity is located or conducted, or where records are kept.

b. Have access to and copy any records that are kept and are relevant to the Project or the requirements of this Order.

c. Inspect any facilities, equipment (including monitoring and control equipment), practices, or operations regulated or required under this Order.

d. Sample or monitor for the purposes of assuring Order compliance.

4. A copy of this Order shall be provided to any consultants, contractors, and subcontractors working on the Project. Copies of this Order shall remain at the Project site for the duration of this Order. The Permittee shall be responsible for work conducted by its consultants, contractors, and any subcontractors.

5. A copy of this Order must be available at the Project site(s) during construction for review by site personnel and agencies. All personnel performing work on the Project shall be familiar with the content of this Order and its posted location at the Project site.

G. Construction

1. Dewatering

a. The Permittee shall develop and maintain on-site a Surface Water Diversion and/or Dewatering Plan(s). The Plan(s) must be developed prior to initiation of any water diversions. The Plan(s) shall include the proposed method and duration of diversion activities and include water quality monitoring conducted, as described in section XIV.C.3, during the entire duration of dewatering and diversion activities. The Plan(s) must be consistent with this Order and must be submitted to the Central Valley Water Board staff at least 30 days prior to implementation.

b. For any temporary dam or other artificial obstruction being constructed, maintained, or placed in operation, sufficient water shall at all times be allowed to pass downstream, to maintain beneficial uses of waters of the state below the dam. Construction, dewatering, and removal of temporary cofferdams shall not violate section XIV.C.3.

c. The temporary dam or other artificial obstruction shall only be built from clean materials such as sandbags, gravel bags, water dams, or clean/washed gravel which will cause little or no siltation.

d. The State Water Resources Control Board (SWRCB) has approved petitions by the Permittee for changes to its San Joaquin River water rights permits and license to facilitate Program-level activities implementing the SJRRP. If Project actions require the Permittee to request changes to its San Joaquin River water right permits, the Permittee will coordinate with the SWRCB regarding this matter. If the SWRCB determines that the Project requires changes to its San Joaquin River water rights permits, the Permittee will file the appropriate petitions with the SWRCB. Any other entities claiming pre-1914 appropriative rights, for which changes to water rights are determined necessary, would make those changes pursuant to California Water Code section 1706.

Water rights associated with the Mendota Pool Bypass and Reach 2B Improvements Project include 11885, 11886, and 11887. This Order is not valid if the Project is not conducted in accordance with an existing water right issued by the State Water Resources Control Board. This Order does not provide a new water right or modify an existing water right.

e. The Permittee shall work with the Central Valley Water Board to obtain coverage under an NPDES permit for dewatering activities that result in discharges into surface water. The Permittee shall work with the Central Valley Water Board to obtain coverage under Waste Discharge Requirements (WDRs), or waiver thereof, for dewatering activities that result in discharges to land.

2. Directional Drilling

a. If installation or relocation of dry and/or wet utility lines is anticipated, the

Permittee shall develop and implement a Dry and Wet Utility Work Plan prior to commencement of dry and wet utility construction. The Dry and Wet Utility Plan must cover all phases of the certified project that will impact waters of the United States and shall be consistent with this Certification.

The Dry and Wet Utility Plan shall include the types of dry and wet utilities to be removed and installed, method and duration of activities, structure configuration, construction materials, equipment, erosion and sediment controls, and a map or drawing indicating the location(s) of dry and wet utility work, as related to any water of the United States in the Project area.

Should the methodology for dry and wet utility work include directional drilling, the Dry and Wet Utility Plan shall incorporate a Directional Drilling Plan to address potential frac-outs. The Directional Drilling Plan shall include, but not be limited to, a description of directional drilling activities, dry and wet utility routes, crossing locations and methods, and other geotechnical considerations (i.e., surficial overburden deposits, clays and shales, bedrock formations, hydrogeology), and a reporting procedure should any level of discharge from a frac-out occur, regardless of the discharge size.

The Directional Drilling Plan must be stamped by a California Registered Geologist or Engineer.

The Utility Work Plan and Direction Drilling Plan must be submitted to the Central Valley Water Board staff at least 30 days prior to implementation.

3. Dredging: Not applicable

4. Fugitive Dust:

Dust abatement activities can cause discharges of sediment to streams and uplands through application of water or other fluids. Dust abatement chemicals added to water can be hazardous to wildlife and, if allowed to enter streams, detrimental to water quality. Therefore, dust abatement activities shall be conducted so that sediment or dust abatement chemicals are not discharged into waters of the state. Dust abatement products or additives that are known to be detrimental to water quality or wildlife shall not be used, unless specific management needs are documented, and product-specific application plans are approved by Central Valley Water Board staff.

5. Good Site Management “Housekeeping”

a. The Permittee shall develop and maintain onsite a project-specific Spill

Prevention, Containment and Cleanup Plan outlining the practices to prevent, minimize, and/or clean up potential spills during construction of the Project. The Plan must detail the Project elements, construction equipment types and location, access and staging and construction sequence. The Plan must be made available to the Central Valley Water Board staff upon request.

b. Refueling of equipment within the floodplain or within 300 feet of the waterway is prohibited. If critical equipment must be refueled within 300 feet of the waterway, spill prevention and countermeasures must be implemented to avoid spills. Refueling areas shall be provided with secondary containment including drip pans and/or placement of absorbent material. No hazardous materials, pesticides, fuels, lubricants, oils, hydraulic fluids, or other construction-related potentially hazardous substances should be stored within a floodplain or within 300 feet of a waterway. The Permittee must perform frequent inspections of construction equipment prior to utilizing it near surface waters to ensure leaks from the equipment are not occurring and are not a threat to water quality.

c. All waste materials resulting from the Project shall be removed from the site and disposed of properly.

6. Hazardous Materials

a. The discharge of petroleum products, any construction materials, hazardous materials, pesticides, fuels, lubricants, oils, hydraulic fluids, raw cement, concrete or the washing thereof, asphalt, paint, coating material, drilling fluids, or other substances potentially hazardous to fish and wildlife resulting from or disturbed by project-related activities is prohibited and shall be prevented from contaminating the soil and/or entering waters of the state. In the event of a prohibited discharge, the Permittee shall comply with notification requirements in sections XIV.B.3.a and XIV.B.3.b.

b. Concrete must be completely cured before coming into contact with waters of the United States and waters of the state. Surface water that contacts wet concrete must be pumped out and disposed of at an appropriate off-site commercial facility, which is authorized to accept concrete wastes.

7. Invasive Species and Soil Borne Pathogens Prior to arrival at the project site and prior to leaving the project site, construction equipment that may contain invasive plants and/or seeds shall be cleaned to reduce the spread of noxious weeds.

8. Post-Construction Storm Water Management- Not applicable

9. Roads

a. The number of access routes, number and size of staging areas, and the total area of the activity must be limited to the minimum necessary to achieve the project goal. Routes and work area boundaries must be clearly demarcated.

b. Temporary materials placed in any water of the state must be removed as soon as construction is completed at that location, and all temporary roads must be removed or re-contoured and restored according to approved re-vegetation and restoration plans.

10. Sediment and Erosion Control

a. Except for activities permitted by the United States Army Corps of

Engineers under Section 404 of the Clean Water Act and/or Section 10 of the Rivers and Harbors Act, soil, silt, or other organic materials shall not be placed where such materials could pass into surface water or surface water drainage courses.

b. Silt fencing, straw wattles, or other effective management practices must be used along the construction zone to minimize soil or sediment along the embankments from migrating into the waters of the state through the entire duration of the Project.

c. The use of netting material (e.g., monofilament-based erosion blankets, plastic netting wrapped straw wattle) that could trap aquatic dependent wildlife is prohibited within the Project area.

d. All areas disturbed by Project activities shall be protected from washout and erosion.

e. Hydroseeding shall be performed with California native seed mix.

11. Special Status Species- Giant garter snake, western pond turtle

12. Storm Water

a. During the construction phase, the Permittee must employ strategies to minimize erosion and the introduction of pollutants into storm water runoff including implementation of an effective combination of erosion and sediment control best management practices prior to the rainy season and during all phases of construction.

H. Site Specific

1. The Permittee shall submit for approval by the Central Valley Water Board Executive Officer, at least 30 days prior to commencement of construction, a final design plan for each Project component with a component-specific Water Quality Management Plan. The Water Quality Monitoring/Management Plan shall include best management practices that will be implemented during construction of that Project component to protect water quality.

2. Water Quality Compliance Plan for Compact Bypass Project – Monitoring for sediment concentration and implementing actions based on the monitoring shall be conducted according to the Water Quality Compliance Plan for Compact Bypass Project, dated October 2020. Monitoring results shall be submitted weekly for the first four weeks following Phase I flow introduction to the Compact Bypass channel, then bi-monthly until Phase II flow introduction.

Monitoring results shall be submitted weekly for the first three weeks following Phase II flow introduction, then bi-monthly for the next three years. Potential non-compliance shall be reported with monitoring reports, and remediation action plans shall be submitted to the Central Valley Water Board staff for approval.

I. Total Maximum Daily Load (TMDL)- Invasive species, pH, boron, chlorpyrifos, DDT, diazinon, group A pesticides, toxicity

J. Mitigation for Temporary Impacts The Permittee shall restore all areas of temporary impacts, including Project site upland areas, which could result in a discharge to waters of the state, to pre-construction contours and conditions.

Total required Project compensatory mitigation information for temporary impacts is summarized in Table 4, [Establishment (Est.), Re-establishment (Re-est.), Rehabilitation (Reh.), Enhancement (Enh.), Preservation (Pres.), Unknown].

Table 4: Required Project Mitigation Quantity for Temporary Impacts by Method Aquatic

Resource Type

Mitigation Type Units Rehabilitation

Wetland Permittee Responsible Acres 19.23 Stream Channel Permittee Responsible Acres 25.49

K. Ecological Restoration and Enhancement The future waters of the United States that are expected to occur within 25 years of the completion of the Project are a combination of created and existing wetlands and other waters of the United States.

Table 5: Total Ecological Restoration and Enhancement Quantity Aquatic

Resource Type

Restoration Type Units Establishment Re-establishment

Wetland Permittee Responsible Acres -- 724

Stream Channel

Permittee Responsible Acres 370 --

L. Certification Deviation

1. Minor modifications of Project locations or predicted impacts may be necessary as a result of unforeseen field conditions, necessary engineering re-design, construction concerns, or similar reasons. Some of these prospective Project modifications may have impacts on water quality. Some modifications of Project locations or predicted impacts may qualify as Certification Deviations as set forth in Attachment F. For purposes of this Certification, a “Certification Deviation” is a Project locational or impact modification that does not require an immediate amendment of the Order, because the Central Valley Water Board has determined that any potential water quality impacts that may result from the change are sufficiently addressed by the Order conditions and the CEQA Findings. After the termination of construction, this Order will be formally amended to reflect all authorized Certification Deviations and any resulting adjustments to the amount of water resource impacts and required compensatory mitigation amounts.

2. A Project modification shall not be granted a Certification Deviation if it warrants or necessitates changes that are not addressed by the Order conditions or the CEQA environmental document such that the Project impacts are not addressed in the Project's environmental document or the conditions of this Order. In this case a supplemental environmental review and different Order will be required.

XV. Water Quality Certification

I hereby issue the Order for the…