SPN Public Notice

Regulatory Division

450 Golden Gate Ave., 4

Floor

San Francisco, CA 94102-

3406

SAN FRANCISCO DISTRICT

PUBLIC NOTICE

PROJECT: Legacy Biosolids Lagoons Cleanup Project

PUBLIC NOTICE NUMBER: 2019-00387S

PUBLIC NOTICE DATE: January 17, 2020

COMMENT S DUE DATE: February 17, 2020

PERMIT MANAGER: Greg Brown T EL EPHONE: 41 5-5 03-6791 E-MAIL: gregory.g.brown@usace.arm y.m il

1. INTRODUCTION: The City of San Jose (POC:

Jessica Donald 408-975-2620), 200 East Santa Clara St,

Floor, San Jose, CA 95113, has applied to the U.S.

Army Corps of Engineers (USACE), San Francisco

Distric t, for a Department of the Army Permit to conduct

cleanup activities at the San Jose-Santa Clara Regional

Wastewater Facility Legacy Biosolids Lagoons. T h is

Department of the Army permit application is being

processed pursuant to the provisions of Section 404 of the

Clean Water Act of 1972, as amended (33 U.S.C. § 1344 et

seq.), and Section 10 of the Rivers and Harbors Ac t of 1899,

as amended (33 U.S.C. § 403 et seq.).

2. PROPOSED PROJECT:

Project Site Location: The project area is located in the

legacy biosolids lagoons immediately north of the San

Jose-Santa Clara Regional Wastewater Facility, at 700 Los

Esteros Road in the City of San Jose, Santa Clara County,

California (figures 1-2). The project area is located in

Township 6 South, Range 1 West, Section 2, on the

Milpitas , CA, USGS 7.5-minute topographic quadrangle

(37.441566°N, -121.942004°W). The project area is

bordered on the north by former salt pond A18, on the west

by the Zanker Road landfill, and on the east by active

biosolids lagoons. California State Route 237 is

approximately 1 mile to the south and Interstate 880

approximately 0.9-mile to the east. Coyote Creek is

approximately 0.6-mile east of the projec t site.

Project Site Description: The proposed project is located

among other diked baylands along the southern end of San

Francisco Bay, between urban areas of San Jose and former

salt evaporation ponds. Land uses adjacent to the project

site consist of industrial uses, including active biosolids

lagoons, landfills, a bomb disposal facility, and other

operational areas of the Regional Wastewater Facility.

Pond A18 is north of the project site and separated from the

project site by an earthen levee. The project site consists of

23 rectangular lagoons totaling approximately 168 acres,

which were constructed and used to collect and store

industrial biosolids between 1962 and 1974. Although the

lagoons have not been used since 1974, material in the

lagoons was graded into windrows in 1998 leaving a series

of linear mounds dominated by ruderal upland vegetation,

interspersed with low areas within each lagoon. Low areas

between the windrows and perimeter dikes of each lagoon

contain a total of 39.49 acres of unvegetated seasonally

ponded waters (salt pannes), and 19.83 acres of nontidal

saline wetlands dominated by pickleweed (Salicornia

pacifica) and salt grass (Distichlis spicata), as shown in

figure 8.

Project Description: The City’s proposed project

would remediate the inactive biosolids lagoons in

c omplianc e w ith Site Cleanup Requirements (SCR) Order

Number R2-2019-0026 issued by the San Francisco Bay

Regional Water Quality Control Board (RWQCB).

Pursuant to the SCR, there is an opportunity to coordinate

this project with the adjacent South San Francisco Bay

Shoreline Project (Shoreline Project). This project is being

implemented by the USACE Civil Works Divis ion w ith

loc al (non-federal) sponsors the Santa Clara Valley Water

Distric t (Valley Water) and the California Coastal

Conservancy. To comply with Shoreline Project timelines,

the lagoon remediation would proceed in two phases.

Phase 1 would prioritize the City’s clean-up of lagoons L-

16 to L-19 in 2020, in time to transfer these lagoons from

the City to Valley Water by January 1, 2021. Advanced

design for Phase 1 is being completed concurrently with

permit application and processing in order to facilitate

incorporation into the Shoreline Projec t. Phase 1 plans

would include the reloc ation of the materials excavated

from lagoons L-16 to L-19 (the shoreline lagoons) into

lagoons L-13 to L-15 (figure 3) for interim stockpiling

pending completion of Phase 2 planning, design and

implementation. Once remediated, lagoons L-16 to L-19

would be included in a Shoreline Project alternate levee

alignment that combines lagoons L-16 to L-19 with Pond

A18 (figure 4).

Phase 2 would complete the cleanup of the remaining

lagoons (L 1-3, 5-7, 9-15, 20-24, and a portion of L-25).

All the excavated materials (inc luding those excavated

during Phase 1) would be consolidated within a portion of

the project site where they would be permanently contained

and capped. Current alternatives being considered for final

consolidation are shown in figure 3. Phase 2 is scheduled

for implementation in 2021-2022. Because of the advanced

timeline for completing Phase 1 design, Phase 2 design is

currently conceptual in nature, and advanced design for

Phase 2 would be completed in late 2020.

Basic Project Purpose: The basic project purpose

comprises the fundamental, essential, or irreducible

purpose of the project, and is used by USACE to determine

whether the project is water dependent. The basic project

purpose is to complete site cleanup of the legacy biosolids

lagoons.

Overall Project Purpose: The overall project purpose

serves as the basis for the Section 404(b)(1) alternatives

analysis and is determined by further defining the basic

project purpose in a manner that more specifically describes

the applicant's goals for the projec t w hile allow ing a

reasonable range of alternatives to be analyzed. The

overall project purpose is to remediate contaminants within

the legacy biosolids lagoons onsite and in compliance with

the RWQCB’s SCR Order, while also delivering the

remediated shoreline lagoons (L-16 to L-19) by January 1,

2021 in time to integrate into the Shoreline Project’s

res toration ac tivities.

Project Impacts: A total of approximately 570,000

cubic yards of legacy biosolids would be excavated from

the lagoons, and placed within a portion of the site for

permanent consolidation, containment, and capping. Phase

1 ac tivities w ould include excavation and/or grading of

approximately 5.99 acres of wetlands and 6.79 acres of

other waters in the shoreline lagoons (L-16 to L-19), and

filling approximately 3.54 acres of wetlands and 5.68 acres

of other waters in lagoons L-13 to L-15. Phase 2 would

include excavation and/or grading approximately 10.29

acres of wetlands and 27.03 acres of other waters in the

remaining lagoons, with a portion of these to be

permanently filled by the consolidated biosolids (figure

10).

Proposed Mitigation: Because the legacy biosolids

requiring cleanup are interspersed with existing aquatic

resources throughout the lagoons, all lagoons would be

impacted by excavation/removal of the biosolids and

therefore complete avoidance of impacts to these aquatic

resources would not be possible. No minimization of

impacts has been proposed, either through selection of

lagoons with fewer aquatic resources for

temporary/permanent placement of excavated biosolids, or

restoration of remaining lagoons once biosolids have been

removed.

The City’s application includes a preliminary

assessment of compensatory mitigation for unavoidable

impac ts to aquatic resources. Because remediation of

ponds L-16 to L-19 would allow the Shoreline Project to

increase the potential enhancement area of pond A18 by

approximately 35 acres, the City has requested

consideration of this factor in their mitigation requirement.

The City’s proposed compensatory mitigation would either

take the form of creation/restoration ac tivities on Fac ility

lands (likely to be focused on seasonal wetlands habitats),

or the purchase of in-kind mitigation credits at an agency-

approved mitigation bank within the region. T he City w ill

develop and submit conceptual mitigation alternatives for

consideration and input by the USACE and RWQCB

during the processing of this permit application.

Project Alternatives: Alternative approaches to meet

SCR requirements have been analyzed in a Closure

Alternatives Analysis Plan by Cornerstone Earth Group,

dated September 25, 2019, including a variety of onsite and

offsite treatment and disposal options. Of these, the

currently proposed approach of consolidating and capping

legacy biosolids within the existing Area of Contamination

(AOC) was found to be the only feasible alternative in light

of current regulatory, time, and cost constraints.

These and other alternatives will need to be further

detailed by the applicant in a 404(b)(1) alternatives

analys is. USACE has not endorsed any submitted

alternatives at this time, and will conduct an independent

review of the project alternatives prior to reaching a final

permit decision.

3. STATE AND LOCAL APPROVALS:

Water Quality Certification: State water quality

certification or a waiver thereof is a prerequisite for the

issuance of a Department of the Army Permit to conduct

any activity which may result in a fill or pollutant discharge

into waters of the United States, pursuant to Section 401 of

the Clean Water Act of 1972, as amended (33 U.S.C. § 1341

et seq.). The applic ant is hereby notified that, unless

USACE is provided documentation indicating a complete

application for water quality certification has been

submitted to the RWQCB within 30 days of this Public

Notice date, the District Engineer may consider the

Department of the Army permit application to be

withdrawn. No Department of the Army Permit w ill be

issued until the applicant obtains the required certification

or a waiver of certification. A waiver can be explicit, or it

may be presumed if the RWQCB fails or refuses to act on

a complete application for water quality certification within

60 days of receipt, unless the District Engineer determines

a shorter or longer period is a reasonable time for the

RWQCB to act.

Water quality issues should be directed to the

Executive Officer, California Regional Water Quality

Control Board, San Francisco Bay Region, 1515 Clay

Street, Suite 1400, Oakland, California 94612, by the close

of the comment period.

Coastal Zone Management: Section 307(c) of the

Coastal Zone Management Act of 1972, as amended (16

U.S.C. § 1456(c) et seq.), requires a non-Federal applicant

seeking a federal license or permit to conduct any activity

occurring in or affecting the coastal zone to obtain a

Consistency Certific ation that indic ates the activity

conforms with the state’s coastal zone management

program. Generally, no federal license or permit will be

granted until the appropriate state agency has issued a

Consistency Certification or has waived its right to do so.

A preliminary review by USACE indicates that the project

is not likely to affect coastal zone resources. T h is

presumption of effect, however, remains subject to a final

determination by the San Francisco Bay Conservation and

Development Commission.

Coastal zone management issues should be directed to

the Executive Director, San Francisco Bay Conservation

and Development Commission, 50 California Street, Suite

2600, San Francisco, California 94111.

Other Local Approvals: The applicant w ill be

applying for the following additional governmental

authorizations for the project: California Department of

Fis h and Wildlife (CDFW) Section 2080/2081

Consultation (Informal Concurrence with Avoidance

Measures and a No Take Determination) under the

California Endangered Species Act, and potentially a

Section 1600 Lake and Streambed Alteration Agreement

(LSAA) for Phase 2.

4. COMPLIANCE WITH VARIOUS FEDERAL

LAWS:

National Environmental Policy Act (NEPA): Upon

review of the Department of the Army permit applic ation

and other supporting documentation, USACE has made a

preliminary determination that the project neither qualifies

for a Categorical Exclusion nor requires the preparation of

an Environmental Impact Statement for the purposes of

NEPA. At the conclusion of the public comment period,

USACE will assess the environmental impacts of the

project in accordance with the requirements of the National

Environmental Policy Act of 1969 (42 U.S.C. §§ 4321-

4347), the Council on Environmental Quality's regulations

at 40 C.F.R. § 1500-1508, and USACE regulations at 33

C.F.R. § 325. The final NEPA analys is w ill normally

address the direct, indirect, and cumulative impacts that

result from regulated activities within the jurisdiction of

USACE and other non-regulated activities USACE

determines to be within its purview of Federal control and

responsibility to justify an expanded scope of analysis for

NEPA purposes. The final NEPA analysis w ill be

incorporated in the decision documentation that provides

the rationale for issuing or denying a Department of the

Army Permit for the project. The final NEPA analysis and

supporting documentation will be on file with the San

Francisco District, Regulatory Division.

Endangered Species Act (ESA): Section 7(a)(2) of

the ESA of 1973, as amended (16 U.S.C. § 1531 et seq.),

requires Federal agencies to consult with either the U.S.

Fis h and Wildlife Servic e (USFWS) or the National Marine

Fis heries Servic e (NMFS) to ensure actions authorized,

funded, or undertaken by the agency are not likely to

jeopardize the continued existence of any Federally-lis ted

species or result in the adverse modification of designated

c ritic al habitat. As the Federal lead agency for this project,

USACE has conducted a review of the California Natural

Diversity Data Base, digital maps prepared by USFWS and

NMFS depicting critical habitat, and other information to

determine the presence or absence of such species and

critical habitat in the project area. Based on this review,

USACE has made a preliminary determination that

Federally-lis ted fish species and designated critical habitat

subject to NMFS oversight are not present at the project

location or in its vicinity and that consultation w ith this

agency w ill not be required. USACE w ill render a final

determination on the need for consultation w ith NMFS at

the close of the comment period, taking into account any

comments provided by NMFS.

As the Federal lead agency for the related Shoreline

Projec t, USACE Civil Works has determined that the

follow ing Federally-lis ted spec ies are present in the project

vic inity and may be affected by project implementation:

Salt-marsh harvest mouse (Reithrodontomys raviventris),

California Least Tern (Sternula antillarum browni),

Ridgway’s rail/California clapper rail (Rallus longirostris

obsoletus), and Western snowy plover (Charadrius nivosus

nivosus). To address project related impacts to these

s pec ies, USACE Civil Works had previously completed

formal consultation with USFWS for the Shoreline Project,

and has re-initiated formal consultation to incorporate

potential effects from Phase 1 and 2 of the remediation

project. Any required consultation must be concluded prior

to the issuance of a Department of the Army Permit for the

project.

Magnuson-Stevens Fishery Conservation and

Management Act (MSFCMA): Section 305(b)(2) of the

MSFCMA of 1966, as amended (16 U.S.C. § 1801 et seq.),

requires Federal agencies to consult with the NMFS on all

proposed actions authorized, funded, or undertaken by the

agency that may adversely affect essential fis h habitat

(EFH). EFH is defined as those waters and substrate

necessary to fish for spawning, breeding, feeding, or

growth to maturity. EFH is designated only for those

species managed under a Federal Fis heries Management

Plan (FMP), such as the Pacific Groundfish FMP, the

Coastal Pelagics FMP, or the Pacific Coast Salmon FMP.

As the Federal lead agency for this project, USACE has

conducted a review of digital maps prepared by NMFS

depicting EFH to determine the presence or absence of EFH

in the project area. Based on this review, USACE has made

a preliminary determination that EFH is not present at the

project location or in its vic inity and that consultation will

not be required. USACE will render a final determination

on the need for consultation at the close of the comment

period, taking into account any comments provided by

NMFS.

Marine Protection, Research, and Sanctuaries Act

(MPRSA): Section 302 of the MPRSA of 1972, as

amended (16 U.S.C. § 1432 et seq.), authorizes the

Secretary of Commerce, in part, to designate areas of ocean

waters, such as the Cordell Bank, Gulf of the Farallones,

and Monterey Bay, as National Marine Sanctuaries for the

purpose of preserving or restoring such areas for their

conservation, recreational, ecological, or aesthetic values.

After such designation, activities in sanctuary waters

authorized under other authorities are valid only if the

Secretary of Commerce certifies that the activities are

consistent with Title III of the Act. No Department of the

Army Permit w ill be issued until the applicant obtains any

required c ertific ation or permit. The project does not occur

in sanctuary waters, and a preliminary review by USACE

indicates the project is not likely to affect sanctuary

resources. This presumption of effect, however, remains

subject to a final determination by the Secretary of

Commerce or his designee.

National Historic Preservation Act (NHPA): Sec tion

106 of the NHPA of 1966, as amended (16 U.S.C. § 470 et

seq.), requires Federal agencies to consult with the

appropriate State Historic Preservation Officer to take into

account the effects of their undertakings on historic

properties listed in or eligible for listing in the National

requires Federal agencies to consult with the appropriate

Tribal Historic Preservation Officer or any Indian tribe to

take into account the effects of their undertakings on

historic properties, including traditional cultural properties,

trust resources, and sacred sites, to which Indian tribes

attach historic, religious, and cultural significance. As the

Federal lead agency for this undertaking, US ACE has

conducted a review of the latest published version of the

National Register of Historic Places, survey information on

file w ith various city and county municipalities, and other

information provided by the applicant to determine the

presence or absence of historic and archaeological

resources within the permit area. Based on this review,

USACE has made a preliminary determination that historic

or archaeological resources may be present near the permit

area, but would not be adversely affected by the project. To

address potential project related impacts to his toric or

archaeological resources, USACE w ill initiate c ons ultation

w ith the State Historic Preservation Officer or the Tribal

Historic Preservation Officer, pursuant to Section 106 of

the Act. Any required consultation must be concluded prior

to the issuance of a Department of the Army Permit for the

project.

5. COMPLI ANCE WI TH THE S ECTI ON 404(b)(1)

GUI DELI NES : Projects resulting in discharges of dredged

or fill material into w aters of the United States must comply

with the Guidelines promulgated by the Administrator of

the Environmental Protection Agency under Section 404(b)

of the Clean Water Act (33 U.S.C. § 1344(b)). An

evaluation pursuant to the Guidelines indicates the project

is dependent on location in or proximity to waters of the

United States to achieve the basic project purpose. T his

conclusion raises the (rebuttable) presumption of the

availability of a practicable alternative to the project that

would result in less adverse impacts to the aquatic

ecosystem while not causing other major adverse

environmental consequences. The applicant has been

informed to submit an analysis of project alternatives to be

reviewed for compliance with the Guidelines.

6. PUBLI C I NTERES T EVALUTI ON: The decision

on whether to issue a Department of the Army Permit w ill

be based on an evaluation of the probable impacts,

including cumulative impacts, of the project and its

intended use on the public interest. Evaluation of the

probable impacts requires a careful weighing of the public

interest factors relevant in each particular case. The

benefits that may accrue from the project must be balanced

against any reasonably foreseeable detriments of project

implementation. The decision on permit is suanc e w ill,

therefore, reflect the national concern for both protection

and utilization of important resources. Public interest

factors which may be relevant to the decision process

include conservation, economics, aesthetics, general

environmental concerns, wetlands, cultural values, fish and

wildlife values, flood hazards, floodplain values, land use,

navigation, shore erosion and accretion, recreation, water

supply and conservation, water quality, energy needs,

safety, food and fiber production, mineral needs,

considerations of property ownership, and, in general, the

needs and welfare of the people.

7. CONSIDERATION OF COMMENTS: USACE is

soliciting comments from the public; Federal, State, and

loc al agenc ies and offic ials; Native American Nations or

other tribal governments; and other interested parties in

order to consider and evaluate the impacts of the project.

All comments received by USACE will be considered in

the decision on whether to issue, modify, condition, or deny

a Department of the Army Permit for the project. To make

this decision, comments are used to assess impacts on

endangered species, historic properties, water quality, and

other environmental or public interest factors addressed in

a final environmental assessment or environmental impact

statement. Comments are also used to determine the need

for a public hearing and to determine the overall public

interest in the project.

8. SUBMI TTI NG CO MMENTS : During the specified

comment period, interested parties may submit written

comments to Greg Brown, San Franc isc o Distric t,

Regulatory Division, 450 Golden Gate Avenue, 4

Floor,

Suite 1111, San Francisco, California 94102-3404;

comment letters should cite the project name, applicant

name, and public notic e number to facilitate review by the

Regulatory Permit Manager. Comments may include a

request for a public hearing on the project prior to a

determination on the Department of the Army permit

application; such requests shall state, with particularity, the

reasons for holding a public hearing. All substantive

comments will be forwarded to the applicant for resolution

or rebuttal. Additional project information or details on any

subsequent project modifications of a minor nature may be

obtained from the applicant and/or agent or by contacting

the Regulatory Permit Manager by telephone or e-mail

(cited in the public notice letterhead). An electronic version

of this public notice may be viewed under the Public

Notices tab on the USACE w ebs ite:

http://www.spn.usace.army.mil/Missions/Regulatory.