HomeMy WebLinkAboutStaff Report 2503-4336CITY OF PALO ALTO
CITY COUNCIL
Monday, April 21, 2025
Council Chambers & Hybrid
5:30 PM
Agenda Item
7.Approval of Amendment No. 1 to the Cooperative Agreement with the Association of Bay
Area Governments to Construct the Horizontal Levee Pilot Project (WQ- 22001) to Reflect
an Additional $2 Million in California Coastal Conservancy Grant Funds; CEQA Status –
Exempt under Section 15133
6
7
4
7
City Council
Staff Report
From: City Manager
Report Type: CONSENT CALENDAR
Lead Department: Public Works
Meeting Date: April 21, 2025
Report #:2503-4336
TITLE
Approval of Amendment No. 1 to the Cooperative Agreement with the Association of Bay Area
Governments to Construct the Horizontal Levee Pilot Project (WQ- 22001) to Reflect an
Additional $2 Million in California Coastal Conservancy Grant Funds; CEQA Status – Exempt
under Section 15133
RECOMMENDATION
Staff recommends that the City Council approve and authorize the City Manager or their
designee to execute Amendment No. 1 to the agreement between the Association of Bay Area
Governments and the City for implementation and construction of the Horizontal Levee Pilot
Project (WQ-22001) to reflect an additional $2 million in grant funding from the California
Coastal Conservancy.
EXECUTIVE SUMMARY
In 2024, the City entered into a Cooperative Agreement with ABAG to formalize responsibilities
of both parties concerning funding, construction, and monitoring of the Horizontal Levee Pilot
Project. The current Cooperative Agreement requires an amendment to account for the
recently awarded California Coastal Conservancy grant. Horizontal levees are a green, nature-
based, multi-beneficial alternative to traditional greyscape solutions (e.g., rip rap, sheet piling)
for wave attenuation on the bayside of flood control levees. Since 2017, the City has been
working in collaboration with the Association of Bay Area Governments (ABAG – host agency
for the San Francisco Estuary Partnership) to design and eventually construct the Horizontal
Levee Pilot Project (WQ-22001) on the east side of Harbor Road near Byxbee Park.
BACKGROUND
Horizontal levees are a nature-based alternative to traditional greyscape solutions (e.g., rip rap,
sheet piling) for wave attenuation on the bayside of flood control levees (Figure 1). Horizontal
levees utilize treated wastewater to irrigate a gently sloping, vegetated ecotone slope that
provides wave attenuation as well as refugia, transitional habitat between tidal wetlands and
6
7
4
7
terrestrial uplands, sea level rise adaptation, and polishing treatment of treated wastewater. A
unique aspect to horizontal levees is their use of treated wastewater to irrigate the ecotone
slope. Other ecotone slopes that have been built in the area utilize passive irrigation or potable
water for irrigation of the vegetated area.
Figure 1: Illustration of a horizontal levee system.
Unlike much of the shoreline along the San Francisco Bay, the Palo Alto shoreline, while highly
developed and altered, continues to sustain tidal marsh. The Palo Alto Baylands shoreline is
comprised of low levees and a closed landfill. Directly behind these levees are City assets that
are critical infrastructure, including the City’s Regional Water Quality Control Plant (RWQCP),
airport, the Palo Alto Flood Basin, roads, and light commercial development. Potential flooding
of City infrastructure, buildings, and other development west of Highway 101 is limited by the
existing levees. However, these levees are not engineered to meet Federal Emergency
Management Agency (FEMA) accreditation standards, and in many locations do not provide
100-year flood protection.
An emerging regional goal and best practice for levee improvement is to incorporate nature-
based solutions, such as horizontal levees, to provide flood protection that can evolve in the
future, restore Bay habitats, and enhance public access. Since design considerations for
horizontal levees are still early in their development, a permanent pilot project was pursued to
answer outstanding questions about permitting requirements, construction costs, and site-
specific design parameters (e.g., plant palettes). Information from Palo Alto’s Horizontal Levee
Pilot Project will inform the design for potential additional future horizontal levees around Palo
Alto and the greater Bay Area.
Since 2017, the City of Palo Alto has collaborated with ABAG – the host entity for the San
Francisco Estuary Partnership – to evaluate and design a permanent horizontal levee pilot
project within the Palo Alto Baylands with the following objectives:
1. Be on the leading edge of integrating habitat enhancement with sea level rise adaptation
and novel wastewater treatment approaches around the San Francisco Bay;
6
7
4
7
2.Integrate a horizontal levee on the bayfront of a traditional flood control levee to provide
wave attenuation;
3.Adapt to sea level rise by providing a vegetated transitional slope that will build organic
soils and support sediment accretion and accumulation to allow for future tidal marsh
migration;
4.Improve habitat along the perimeter of Harbor Marsh for native species;
5.Provide polishing treatment to treated wastewater; and
6.Maintain and provide opportunities for compatible low-impact recreation and social
infrastructure.
On January 22, 2024, the City Council adopted Ordinance No. 5616,1 Approving a Plan for
Improvements to the Palo Alto Baylands as part of the Horizontal Levee Pilot Project that
includes:
1.construction of a berm and horizontal levee along a portion of existing, poor-quality
upland habitat adjacent to Harbor Marsh within the Palo Alto Baylands Nature Preserve;
2.installation of various native plants on the Project site to restore diverse transitional
habitats including freshwater marsh, wet meadow, and riparian scrub;
3.installation of an underground pipeline to transport treated wastewater along
Embarcadero and Harbor Roads to the horizontal levee for native plant irrigation;
4.realignment of a portion of the Marsh Front Trail as required to accommodate the
horizontal levee and reconnect habitats; and
5.installation of educational signage and provide opportunities for public participation in
community science activities.
The City entered into a Cooperative Agreement with ABAG pursuant to Council approval and
authorization1 in 2024 that divided responsibilities between the agencies accordingly:
1.ABAG will use grant funding it obtained to provide Project construction, construction
management, and related permit compliance;
2.the City will actively participate during project construction and provide oversight of
change orders and budget overruns, assist with public outreach, obtain and pay for
required construction permits, implement the Monitoring and Adaptive Management
Plan, and once constructed, own and operate the Project.
1 City Council, January 22, 2024; Agenda Item #5, SR #2303-1230,
https://recordsportal.paloalto.gov/Weblink/DocView.aspx?id=82647
6
7
4
7
ANALYSIS
Funding sources for Horizontal Levee Pilot Project (WQ-22001) construction at time of
Cooperative Agreement approval were from the Environmental Protection Agency (EPA)
Breaking Ground, Nature Based Solutions for Resilient Shorelines, and National Estuary
Program Bipartisan Infrastructure Law grants. These grants were awarded to and are
administered by ABAG and required local match of in-kind services (e.g., non-monetary
contribution) from the City of $3.4 million, which the City was to provide by showing proof of
expenditures in the RWQCP’s Capital Improvement Program projects. The project was bid
through ABAG in Spring 2024 and received three bids for construction that exceeded the total
available budget at the time. Since then, the bids expired while the project team evaluated
ways to decrease construction costs (e.g., bidding earlier in the year) as well as ways to increase
available budget (e.g., pursue additional grant opportunities). In November 2024, the California
Coastal Conservancy awarded ABAG $2 million to construct the Project with no local match
requirement. Amendment No. 1 (Attachment A) to the Cooperative Agreement between ABAG
and the City includes modifications in several locations to account for this additional funding
source.
With the addition of California Coastal Conservancy funds, the project has a total of $4.9 million
available for construction and construction management (see below table for detailed
breakdown of project funding including the changes described in this report). The proposed
amendment to the Cooperative Agreement adds the California Coastal Conservancy grant of $2
million to the ABAG contributions to the project and decreases the City’s required local match
for construction from $3.4 million to $1.4 million to be provided in-kind from Long Range
Facilities Plan Update expenses instead of expenses from the Local Advanced Water Purification
Facility project. The project was re-bid in early 2025 and received four bids within the new
construction budget. Construction is anticipated to begin in Spring 2025 and end in early 2026.
6
7
4
7
6
7
4
7
FISCAL/RESOURCE IMPACT
2 and others for required monitoring, and another $0.2
million is recommended to be funded in future years for the project. Funding in future years is
subject to Council approval as part of the annual budget appropriation process.
STAKEHOLDER ENGAGEMENT
ENVIRONMENTAL REVIEW
ATTACHMENTS
APPROVED BY: Brad Eggleston, Director Public Works/City Engineer
2 City Council, April 22, 2024; Agenda Item #9, SR #2402-2683,
AMENDMENT NO. 1
This AMENDMENT, effective January 1, 2025, is Amendment No. 1 to the COOPERATIVE
AGREEMENT (“Agreement”) entered into and effective as of January 26, 2024, by and between the
ASSOCIATION OF BAY AREA GOVERNMENTS (“ABAG”) and the CITY OF PALO ALTO
(“City”), individually referred to herein as “Party” and together as “Parties.”
NOW, THEREFORE, the parties agree to modify the subject Agreement as indicated below.
Where modifications have been made, added text is indicated in italics, deleted text is indicated in
strikethrough format.
1. Recital D. is revised to include a new funding source, as follows:
D. WHEREAS, ABAG has received funding via
•United States Environmental Protection Agency (EPA) Grant #W9-98T55001
(“Breaking Ground Grant”), Date of Award May 8, 2023, in the amount of eight
million, six hundred fifty-eight thousand, nine hundred eighteen dollars ($8,658,918),
•EPA Grant #W9-98T20401 (“Nature Based Solutions (NBS) for Resilient Shorelines
Grant”), Date of Award September 13, 2021, in the amount of three million, seven
hundred eighty-two thousand, eight hundred eighteen dollars ($3,782,818) a portion
of which will be used in the completion of this project,
•EPA Grant #4T-98T45901 (“National Estuary Program Bipartisan Infrastructure
Law Grant”) in the amount of nine hundred nine thousand eight hundred dollars
($909,800), a portion of which will be used in the completion of this project, and
•State of California Coastal Conservancy (SCC) Grant G24-046 in the amount of two
million dollars ($2,000,000).
All three four grants allow for no-cost extensions possible up to approximately four
(4) years beyond the completion dates as contemplated by the Grants; and
2. Recital E is revised to include a new funding source, as follows:
E. WHEREAS, Parties’ respective funding contributions to the PROJECT (excluding
City staff time) are as follows:
ABAG/City of Palo Alto
Project
Phase
ABAG
Contribution
Source(s) of ABAG
Funding
City
Contribution
Source(s) of City
Funding
Preliminary
Design
(completed)
$620,673 (paid)
•Integrated Regional
Water Management
Program Grant
•State Coastal
Conservancy
Proposition 1 Grant
$275,000
(paid)
Wastewater
Treatment Plant
Fund and Secondary
Treatment Upgrades
Project
Design &
Permitting
(99%
complete)
$763,661
$563,660 (paid)
•EPA NBS for
Resilient Shorelines
Grant
•EPA Bipartisan
Infrastructure Law
Funding
$1,316,794.29
(paid)
Wastewater
Treatment Plant
Fund and Secondary
Treatment Upgrades
Projecta
Construction
&
Construction
Management
$3,073,882
$4,860,846
(pending)
•EPA NBS for
Resilient Shorelines
Grant
•EPA Breaking
Ground Grant
•EPA NEP Bipartisan
Infrastructure Law
Funding
•State Coastal
Conservancy
$3,429,459
$1,429,459
(pending)
Local Advanced
Water Purification
Facility Project
Long Range
Facilities Plan
Updatea
Post-
construction
Monitoring
& Reporting
$0 Not Applicable $777,055
(pending)
Wastewater
Treatment Plant
Fund
Operation &
Maintenance $0 Not Applicable Unknown
Wastewater
Treatment Plant
Fund
aCity is leveraging funds spent on planned Capital Improvements that are occurring upstream of the
PROJECT at the wastewater treatment plant; actual out-of-pocket expenses for this project are lower
than reported in this table.
3. Recital G is revised to adjust ABAG’s contribution:
G. WHEREAS, for construction and post-construction phases, ABAG will contribute a
total of $3,073,882 $4,860,846 towards the PROJECT, as further described in Appendix A;
and
4. Recital H is revised to adjust City’s contribution:
ABAG/City of Palo Alto
H. WHEREAS, for construction and post-construction phases, the City will contribute a
total of $4,206,514 $2,206,514 (including the required $3,429,459 $1,429,459 in matching
funds for the Breaking Ground Grant); and
5. Section 1, ABAG Obligations, Article 1.3 is revised as shown:
1.3 ABAG will promptly notify City of the discovery of hazardous materials at the
Property. ABAG and the City will jointly evaluate the severity and extent of the hazardous
materials contamination at the Property and decide on the appropriate course of action to
remediate the contamination pursuant to federal and state laws and regulations. ABAG and
the City will reassess the feasibility of the PROJECT and mutually agree on a course of
action prior to the commencement of additional work. Should the Parties conclude the
PROJECT is no longer feasible financially with the available EPA and State Coastal
Conservancy Grants’ funding, the Parties may, individually or collectively, terminate
proceeding with the PROJECT. Should EPA and State Coastal Conservancy Grants’ funding
be cancelled, or approval withdrawn as a result of such termination, the City shall be fully
and solely responsible for all costs incurred for the PROJECT.
6. Section II, City of Palo Alto Obligations, Article 2.3 is revised as shown:
The City shall provide appropriate documentation to ABAG of the required
Breaking Ground Grant funding match obligation in the amount of three million, four
hundred twenty-nine thousand, four hundred fifty-nine dollars ($3,429,459). one million,
four hundred twenty-nine thousand, four hundred fifty-nine dollars ($1,429,459).
7. Appendix A: Project Description and Scope of Work is removed in its entirety and replaced
with Appendix A: Project Description and Scope of Work, (Revised January 1, 2025).
8. Retention of Contract Provisions. Except as provided herein, all other terms and conditions of the
Agreement remain unchanged.
IN WITNESS WHEREOF, this Agreement has been executed by the Parties hereto on the date first
above written.
ASSOCIATION OF BAY AREA GOVERNMENTS CITY OF PALO ALTO
Andrew B. Fremier, Metropolitan Transportation
Commission Executive Director, Acting pursuant to
the Contract for Services dated May 30, 2017
Ed Shikada, City Manager
ABAG/City of Palo Alto
APPENDIX A
(Revised January 1, 2025)
Figure 1 Palo Alto Horizontal Levee Rendering
The Palo Alto Horizontal Levee Pilot (PAHLP) project is a novel initiative led by the City of Palo
Alto and the San Francisco Estuary Partnership. The goals of the Project are to enhance the ecological
function of the project site and improve resilience to sea level rise. The project objectives include:
• Improve habitat along the perimeter of Harbor Marsh for native species;
• Restore rare and historic broad ecotone that supports a variety of transitional plant
assemblages;
• Determine design standards, permitting requirements, and extent of maintenance for
incorporation into the future larger levee improvement project (i.e., SAFER Bay/Shoreline
Study);
• Adapt to sea level rise by providing a transitional slope that will support freshwater plants,
which in turn build organic soils, all of which is aimed at keeping pace with sea level rise;
• Maintain public access to the existing trail system while providing opportunities for
compatible low-impact recreation, increased social infrastructure, and educational
opportunities on sea level rise and other topics;
• Ensure perspectives of marginalized communities are incorporated into social infrastructure
and educational components; and
ABAG/City of Palo Alto
• Provide polishing treatment to discharged treated wastewater.
The Project site is directly adjacent to the City’s Regional Water Quality Control Plant
(“RWQCP”) and Byxbee Park. The Project location is also adjacent to the existing Harbor Marsh, an
approximately 90-acre tidal saltmarsh that was established within the former Palo Alto Yacht Harbor. The
Project site is bounded by Harbor Marsh to the east, Embarcadero Road to the north, the RWQCP and
Harbor Road to the west, and the Byxbee Park parking lot entrance to the south. The project location
includes a 500-linear-foot (LF) proposed levee berm, including 315 linear feet of treatment zone irrigated
with treated wastewater to create a transitional freshwater wetland slope with upland/riparian transitional
plantings in adjacent areas supported with limited irrigation. A 1,650-LF treated wastewater pipeline will
be buried along Harbor Road and Embarcadero Road north and west of the proposed levee, connecting to
a new supply pump at the City of Palo Alto Regional Water Quality Control Plant (RWQCP), located at
2501 Embarcadero Way, Palo Alto, California 94303. The horizontal levee itself would have a variety of
freshwater marsh, wet meadow, and riparian/upland scrub ecotypes. As the freshwater inputs enter the
marsh plain, a brackish marsh ecotone band is expected to form within the salt marsh immediately
adjacent to the horizontal levee.
The horizontal levee would be divided into four primary areas: (1) an engineered levee berm to
support the horizontal levee slope; (2) a treatment zone designed to support polishing of treated
wastewater via subsurface seepage through a drainage layer while supporting native transitional habitats;
(3) a downslope habitat zone designed to support a variety of ecotypes where polished wastewater would
seep toward the adjacent Harbor Marsh as shallow surface/subsurface flow; and (4) transitional slopes
north and south of the treatment zone where the project conforms to the existing bank line. The horizontal
levee is designed to be a freshwater ecotone transition zone to the tidal marsh.
The City of Palo Alto is the permittee on all permits which have been issued:
Permit Dated
Federal Aviation Administration (FAA) – Determination of No Hazard to Air
Navigation (Aeronautical Study No. 2023-AWP-6606-OE)5/11/2023
Federal Aviation Administration (FAA) – Determination of No Hazard to Air
Navigation for Temporary Structure (Aeronautical Study No. 2023-AWP-12517-
OE)
8/29/2023
National Marine Fisheries Service (NMFS) – Letter of Concurrence (with 'not
likely to adversely affect' determination) (WCRO-2023-00141)4/20/2023
SF Bay Regional Water Quality Control Board – Clean Water Action Section 401
General Water Quality Certification for Small Habitat Restoration Projects (File
No. SB12006GN; WDID# 2 CW451131)
8/1/2023
San Francisco Bay Conservation and Development Commission – Amendment to
Major Permit (M1999.043, Amendment No. 6)4/5/24
ABAG/City of Palo Alto
United States Army Corps of Engineers (USACE) – Nationwide Permit 27 (SPN-
2019-00445) Aquatic Habitat Restoration, Enhancement, and Establishment
Activities
5/5/2023
United States Fish and Wildlife Service (USFWS) – Programmatic Biological and
Conference Opinion ESA Section 7(a)(2) Review Form (2022-0005149-S7)3/31/2023
California Department of Fish and Wildlife – Restoration Management Permit
(RMP 2023-0008-R3)12/15/2023
City of Palo Alto – Minor Architectural Review (23PLN-00043)11/30/2023
City of Palo Alto – Street Work Permit (to be obtained by the construction firm) PENDING
State Water Resources Control Board – General Permit for Discharges of Storm
Water Runoff Associated with Construction Activity (to be obtained by the
construction firm)
PENDING
On December 19, 2023, the City issued a Notice of Exemption that the PROJECT was exempt from
review under the California Environmental Quality Act (“CEQA”) (Cal. Public Resources Code § 21000,
et seq.) pursuant to CEQA Guideline Section 15333 because the PROJECT qualifies as a small habitat
restoration project.
Table A: Outstanding Work to be Paid for by ABAG
Party Name Service Provided
Responsible
Entity
Projected
Budget Amount
Zoon Engineering
Construction Management Services
Contract ABAG $427,937
TBD Construction Services Contract ABAG $4,121,055
Save The Bay
Plant propagation, planting, community
outreach ABAG $131,854
TBD Contingency ABAG $180,000
TOTAL $4,860,846
Table B: Palo Alto Horizontal Levee Pilot – Design, Community Engagement, and Implementation
Process
Task Status Funder
Phase 1 – Early Design Concepts and Stakeholder Engagement - 2017 - 2020
Feasibility Study Completed Oro Loma Sanitary District
ABAG/City of Palo Alto
30% Design Completed EPA Climate Ready Estuaries
Planning and Stakeholder
Outreach (carried over from
Phase 1 and 2)
Completed State Coastal Conservancy
Phase 2 – Design and Permitting – 2020-2025
Permitting studies,
Geotechnical Report Completed City of Palo Alto
60% Design, Construction
Budget and Permitting Memo Completed
BRRIT Consultations –
including pre-permitting
consultation in June, 2022
Completed
Permit Applications See Permit Table
State Coastal Conservancy and
EPA Water Quality
Improvement Fund Grant #
#W9-98T55001
Permit Fees Completed City of Palo Alto
CEQA - Categorical
Exemption Completed City of Palo Alto
QAPP Completed
100% Design, including final
design specifications, bid
package and bid period support
Scheduled for completion early
2025
EPA Water Quality
Improvement Fund Grant #
#W9-98T55001
Phase 3 – Construction, Stewardship, Monitoring and Outreach – 2024-2026
Plant Propagation, Community
Outreach and Planting – Save
The Bay
Construction management and
monitoring
In progress
EPA Water Quality
Improvement Fund (#W9-
98T55001)
Construction In progress
EPA Water Quality
Improvement Fund (#W9-
98T20401)
State Coastal Conservancy
Grant (Grant #G24-046)
Phase 4 – Monitoring & Reporting – 2023-2029
Community Science &
Monitoring In progress
EPA Water Quality
Improvement Fund (#W9-
98T20401)
Salt Marsh Harvest Mouse Site
Utilization Studies In progress City of Palo Alto
Sediment Accretion Study In progress City of Palo Alto
Photo-point Monitoring In progress City of Palo Alto
ABAG/City of Palo Alto
Vegetation Surveys,
Vegetation Establishment, and
Habitat Type Evaluations
To be started after construction City of Palo Alto
Benthic Community
Monitoring To be started after construction City of Palo Alto
Wastewater Effluent and
Volume Monitoring In progress City of Palo Alto