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SPK-2009-01483, Proposal to Reissue Department of the Army Permit for the California High-Speed Rail, Merced to Fresno Section, Permit Package 1 project, Fresno and Madera Counties, CA

Regulatory Division
Published April 5, 2019
Expiration date: 4/20/2019

Comments Period: April 8, 2019 – April 20, 2019

SUBJECT: The U.S. Army Corps of Engineers, Sacramento District, (Corps) is evaluating a request by the California High-Speed Rail Authority (Authority) to reissue a Department of the Army (DA) permit for construction of Permit Package 1 (PP1) of the California High-Speed Rail (HSR) Merced to Fresno Section (M-F) project. The DA permit for PP1 was originally issued on March 13, 2014, and expired on April 1, 2019. The Authority has not proposed changes to the scope of the project, the environmental or construction footprints, or project impacts, from those that were previously authorized by the Corps. The previously issued PP1 permit, as modified, authorized the permanent discharge of fill material into 1.63 acres of wetlands (e.g. vernal pools, seasonal wetlands, palustrine forested wetlands, freshwater marsh) and 7.78 acres of other waters of the U.S. (e.g. natural riverine, constructed channels, constructed basins, open water), and the temporary discharge of fill material into 18.83 acres of other waters of the U.S. This notice is to inform interested parties of the proposed permit reissuance and to solicit comments.

AUTHORITY: This application is being evaluated under Section 404 of the Clean Water Act for the discharge of dredged or fill material in waters of the United States.

APPLICANT: State of California, California High-Speed Rail Authority, Attn: Mr. Mark McLoughlin, 770 L Street, Suite 800, Sacramento, California 95814-3359

LOCATION: PP1 is an approximately 24.1-mile segment of the California HSR project, located at the southern end of the approximately 65-mile Merced to Fresno Section. The PP1 alignment begins on the west side of the Burlington Northern Santa Fe (BNSF) tracks immediately south of Avenue 17, (Latitude 36.995433°, Longitude -120.042872°) in Madera, Madera County, and travels southeast along the west side of the BNSF tracks until Cottonwood Creek. South of Cottonwood Creek the alignment turns south towards the Union Pacific Railroad (UPRR) tracks and joins the UPRR corridor north of the San Joaquin Corridor. The alignment crosses over the San Joaquin River and UPRR tracks and continues on the west side of the UPRR tracks through Fresno, ending on the west side of the UPRR tracks south of State Route 41 at Los Angeles Street, (Latitude 36.723642°, Longitude -119.784803°) in Fresno, Fresno County, California. The project is within Madera and Fresno counties.

PROJECT DESCRIPTION: The California High-Speed Rail Authority proposes to continue their previously authorized permanent discharge of fill material into a total of 1.63 acres of wetlands and 7.78 acres of other waters of the U.S., and the temporary discharge of fill material into 18.83 acres of other waters of the U.S., in order to construct, operate, and maintain an electric-powered High-Speed Rail system in California. When completed, the nearly 800-mile train system would provide new passenger rail service to more than 90% of the state’s population, connecting the major population centers of Sacramento, the San Francisco Bay Area, the Central Valley, Los Angeles, the Inland Empire, Orange County, and San Diego. More than 200 weekday trains would serve the statewide intercity travel market. The HSR system includes the HSR tracks, structures, stations, traction power substations, and maintenance facilities and train vehicles. The HSR System is envisioned as a state-of-the-art, electrically powered, high-speed, steel-wheel-on-steel-rail technology, which would include the latest technology, safety, signaling, and automated train-control systems. The fully grade-separated, dedicated track alignment would allow operating speeds of up to 220 miles per hour, and make a trip from Los Angeles to San Francisco in approximately 2 hours and 40 minutes.

The Merced to Fresno Section, located in the San Joaquin Valley, is one of nine sections identified in the Statewide Programmatic EIR/EIS completed by the Authority and Federal Railroad Administration (FRA) in 2005. The PP1 project would involve construction of a 24.1-mile segment of the Merced to Fresno Section, including the Fresno Mariposa Street station and associated facilities. The permit area includes two fully grade-separated tracks within a 100-foot right-of-way, associated facilities, and portions of existing surface streets that would be realigned or modified to cross the alignment. The alignment would be largely at-grade (18.7 miles), with sections above grade on retained-fill embankment (1.4 miles) and elevated structures (2.4 miles), as well as a section below grade (1.6 miles). The PP1 segment starts at-grade for approximately 0.5 mile before transitioning to retained fill embankment for 0.4 mile, then rises to an elevated structure over the Fresno River for 0.5 mile. The alignment then transitions back to retained fill embankment for 0.4 mile, and continues at-grade for 10.0 miles. As the alignment approaches the San Joaquin River, it rises to retained fill embankment for 0.3 mile, then transitions to elevated structure for 1.9 miles. The alignment then transitions to retained fill embankment for 0.3 mile, and continues at-grade for 6.9 miles. Within the City of Fresno, the alignment drops below grade for 1.6 miles, then rises back to grade for the remaining 1.3 miles and entry into the downtown Fresno Mariposa Street station. Associated facilities include one 32,000-square foot traction power station, two 9,600-square foot switching stations, and six 8,000-square foot paralleling stations. The source of all fill material would either come from permitted, commercial sources, or would be generated on-site as part of a balanced cut-and-fill operation, provided the cut material is clean and of proper quality to be used as fill.

The overall project purpose is to implement the Merced to Fresno Section of the California HSR System to provide the public with electric-powered high-speed rail service that provides predictable and consistent travel times between major urban centers and connectivity to airports, mass transit, and the highway network in the central San Joaquin Valley, and to connect the northern and southern portions of the system. The applicant believes a need for an HSR system exists statewide as the capacity of California’s intercity transportation system, including the central San Joaquin Valley region, is insufficient to meet future travel demands, and the current and projected future congestion of the system is expected to result in continued deterioration of air quality, reduced reliability, and increased travel times.


Background: The FRA is the lead Federal agency for compliance with NEPA, the Endangered Species Act (ESA), and the National Historic Preservation Act (NHPA), for the HSR System. The Corps, the U.S. Environmental Protection Agency (USEPA), the FRA, and the Authority signed a Memorandum of Understanding (MOU) in December of 2010, creating an integrated process for compliance with NEPA, the Clean Water Act, and the Rivers and Harbors Act. The MOU includes a series of checkpoints to determine the least environmentally damaging practicable alternative (LEDPA), resulting in an integrated NEPA document meeting the needs of the FRA and the Corps. An EIR/EIS was prepared for the Merced to Fresno Section by FRA and the Authority with the Corps as a cooperating agency. The Final EIR/EIS was published in April 2012, and an addendum and errata to the Final EIR/EIS was released on April 27, 2012. FRA signed a ROD and General Conformity Determination on September 18, 2012. A copy of the Final EIR/EIS can be found on the Authority’s website at 

For the proposed action under consideration, the Corps prepared a Record of Decision (ROD) containing an analysis of the entire 24.1-mile PP1 segment on March 13, 2014. The Corps’ ROD adopted the M-F Section Final EIR/EIS, and included a public interest review and Section 404(b)(1) Guidelines analysis for the 24.1-mile PP1 segment. A DA permit, authorizing construction of 22.3 miles of PP1 from Avenue 15 ¾ in Madera County through the Fresno Station, was issued the same day. The remaining northern 1.8 miles of PP1 analyzed in the Corps’ ROD but not authorized by the original PP1 permit included a crossing of the Fresno River. Section 408 permission under Section 14 of the Rivers and Harbors Act of 1899 was required for this crossing, but had not been obtained at the time of DA permit issuance. Section 408 permission was received on April 28, 2015, and the PP1 permit was modified to include the 1.8-mile Fresno River crossing from Avenue 17 to Avenue 15 ¾ on May 19, 2015.

The March 13, 2014, PP1 permit authorized the permanent discharge of fill material into 1.63 acres of wetlands and 5.33 acres of other waters of the U.S., and the temporary discharge of fill material into 3.86 acres of other waters of the U.S. The PP1 permit has been modified a total of ten times. The permit modifications were issued on April 15, 2014; May 19, 2015; June 12, 2015; July 7, 2015; July 15, 2015; September 2, 2015; December 7, 2015; April 14, 2016; May 6, 2016; and November 27, 2018. Four of the above modifications changed the project description to incorporate final designs at specific locations as informed by geotechnical work and coordination with third parties including utilities, counties, property owners, and the City of Fresno, and/or included design refinements allowing for additional temporary construction access and staging, temporary traffic realignments, utility relocations, or permanent access. These four modifications included expansions of the project footprint and increases in discharges of fill material into waters of the U.S. (WOUS). The remaining six modifications extended the deadline for the mitigation documents required by Special Condition 4 of the PP1 permit.

Modifications to the PP1 permit authorizing expansion of the project footprint and/or increases in discharges of fill material into WOUS are detailed in Table 1:

Table 1.

Date of permit modification

Expansion of project footprint

Increased discharge of permanent fill into WOUS (acres)

Increased discharge of temporary fill into WOUS (acres)

May 19, 2015

1.8 miles of alignment



July 7, 2015

51.98 acres



April 14, 2016

708 acres



November 27, 2018

1.67 acres




Accounting for the original PP1 permit and all permit modifications to-date, the Corps authorized the permanent discharge of fill material into a total of 1.63 acres of wetlands and 7.78 acres of other waters of the U.S., and the temporary discharge of fill material into 18.83 acres of other waters of the U.S.

The applicant is currently constructing the HSR System authorized in 2014, and a number of the proposed discharges into waters of the U.S. have already occurred.

Environmental Setting. Typical land uses occurring within the PP1 project footprint include agricultural, rural residential, and urban (industrial, commercial, and residential). Some undeveloped natural areas occur along the alignment, including Camp Pashayan (within the San Joaquin Ecological Reserve). Types of aquatic resources within the proposed project footprint, as modified, include vernal pools, seasonal wetlands, palustrine forested wetlands, freshwater marsh, natural riverine channels, constructed channels, constructed retention/detention basins, and open water. Within the larger approximately 23,900-acre M-F Section review area, the Corps has verified approximately 129 acres of wetlands and 312 acres of other waters of the U.S.

Alternatives. Six alternatives were analyzed within the M-F Section EIR/EIS, including two alternatives within PP1. Through the multi-agency review process and response to comments on the draft EIR/EIS, a preferred alternative and preliminary Least Environmentally Damaging Practicable Alternative (LEDPA) was identified in the M-F Section Final EIR/EIS. The Hybrid alternative, which includes the Fresno Mariposa Street Station and Downtown Merced Station location alternatives, is the proposed project and represents the applicant’s preferred alternative. The Corps determined that the Hybrid alternative was the LEDPA in our March 13, 2014 ROD, and issued a DA permit authorizing construction of 22.3 miles of PP1 on the same date. The remaining 1.8 miles of PP1 were authorized via permit modification on May 19, 2015.

Mitigation. The Corps requires that applicants consider and use all reasonable and practical measures to avoid and minimize impacts to aquatic resources. If the applicant is unable to avoid or minimize all impacts, the Corps may require compensatory mitigation. The Authority has submitted, and the Corps has approved, a permittee-responsible on- and off-site mitigation plan for permanent and temporary impacts to wetlands and other waters of the U.S. resulting from construction of PP1. The project as modified to-date, would result in 9.41 acres of unavoidable permanent impacts and 18.83 acres of unavoidable temporary impacts to wetlands and other waters of the U.S. The Corps required the Authority to compensate for the permanent impacts via construction of 10.16 acres of vernal pool wetlands at the Lazy K Ranch mitigation site. The required compensatory mitigation ratios for permanent impacts were established using the January 23, 2012, 12501-SPD Regulatory Program Standard Operating Procedure for Determination of Mitigation Ratios. The Corps also required the Authority to restore all temporary impacts to pre-project condition. As of the date of this public notice, the Corps has determined that Authority is in compliance with the above mitigation requirements. A reissued permit for PP1 would be consistent with the mitigation requirements of the previously issued permit and subsequent permit modifications.

OTHER GOVERNMENTAL AUTHORIZATIONS: The September 14, 2012, U.S. Fish and Wildlife Service Biological Opinion (Number 08ESMF00-2012-F-0248), as amended, is valid and covers the permit area and the proposed activities. The April 17, 2012, National Marine Fisheries Service Biological Opinion (Number 2011/05794) is valid and covers the permit area and the proposed activities. The July 22, 2011, National Historic Preservation Act Section 106 Programmatic Agreement and the August 31, 2012, Memorandum of Agreement, as amended, are valid and cover the permit area and the proposed activities. The March 12, 2014, Section 401 Water Quality Certification (SB13001IN, RM # 391375), as amended, is valid and covers the permit area and the proposed activities.

EVALUATION FACTORS: The decision whether to issue a permit will be based on an evaluation of the probable impacts, including cumulative impacts, of the described activity on the public interest. That decision will reflect the national concern for both protection and utilization of important resources. The benefit, which reasonably may be expected to accrue from the described activity, must be balanced against its reasonably foreseeable detriments. All factors which may be relevant to the described activity will be considered, including the cumulative effects thereof; among those are conservation, economics, aesthetics, general environmental concerns, wetlands, historic properties, fish and wildlife values, flood hazards, floodplain values, land use, navigation, shoreline erosion and accretion, recreation, water supply and conservation, water quality, energy needs, safety, food and fiber production, mineral needs, consideration of property ownership and, in general, the needs and welfare of the people. The activity's impact on the public interest will include application of the Section 404(b)(1) guidelines promulgated by the Administrator, Environmental Protection Agency (40 CFR Part 230).

The Corps is soliciting comments from the public, Federal, State, and local agencies and officials, Indian tribes, and other interested parties in order to consider and evaluate the impacts of this proposed activity. Any comments received will be considered by the Corps to determine whether to issue, modify, condition, or deny a permit for this proposal. To make this decision, comments are used to assess impacts on endangered species, historic properties, water quality, general environmental effects, and other public interest factors listed above. Comments are used in the preparation of an Environmental Assessment and/or an Environmental Impact Statement pursuant to the National Environmental Policy Act. Comments are also used to determine the need for a public hearing and to determine the overall public interest of the proposed activity.

SUBMITTING COMMENTS: Written comments, referencing Public Notice SPK-2009-01483 must be submitted to the office listed below on or before April 20, 2019.

Mr. Zachary Fancher, Senior Project Manager
US Army Corps of Engineers, Sacramento District
1325 J Street, Suite 1350
Sacramento, California 95814-2922

The Corps is particularly interested in receiving comments related to the proposal's probable impacts on the affected aquatic environment and the secondary and cumulative effects. Anyone may request, in writing, that a public hearing be held to consider this application. Requests shall specifically state, with particularity, the reason(s) for holding a public hearing. If the Corps determines that the information received in response to this notice is inadequate for thorough evaluation, a public hearing may be warranted. If a public hearing is warranted, interested parties will be notified of the time, date, and location. Please note that all comment letters received are subject to release to the public through the Freedom of Information Act. If you have questions or need additional information please contact the applicant or the Corps' project manager, Mr. Zachary Fancher, (916) 557-6643,

Attachments: 26 maps