State of California
Memorandum

To: Eric Larson and George Neillands Date: August 20, 2009
From: Kristine Atkinson
Department of Fish and Game
Central Coast Region, P.O. Box 999
Santa Cruz, CA 95060
Subject: Outcome from USFWS, NOAA Fisheries, and CDFG Coordination Meetings (April 21
through August 20, 2009) discussing our vision of restoration of the Pescadero Marsh,
San Mateo County.

USFWS staff (John Klochak), NOAA Fisheries staff (John McKeon, Kit Crump, and Bill
Stevens), CDFG staff (Kristine Atkinson, George Neillands, and Eric Larson) met to coordinate
our vision of restoration of the Pescadero Marsh, San Mateo County.

The following is a list of outcomes of these meetings:

a) We agreed, in concept, to restore Pescadero Marsh to, a healthy, functioning state
characterized by an extensive freshwater lagoon, marsh, and pond habitats during the
summer and fall so that they can support healthy populations of native species. We
recognize that there will be constraints to the amount of habitat that the site can sustain
associated with hydrological and geomorphic processes operating at the
landscape/watershed scale, along with anthropogenic disruptions to these processes.
Additionally, we recognize that this system is dynamic and will constantly change over
time. We will develop biological goals appropriate to these processes and constraints
and the dynamic nature of this system. Watershed processes that support habitat
conditions may not dictate 100% of what we do, but understanding and taking into
account these processes involved as well as the disruptions to those processes that
may limit what happens biologically is recognized as crucial to restoration at Pescadero
Lagoon.

b) We agreed that restoring the biological function of Pescadero Creek Estuary / Lagoon
requires an “ecological approach” and should focus on specific target species. Our list
of target species requires further discussion but so far includes the following: coho
salmon, a species Federal Endangered Species Act (FESA) and California Endangered
Species Act (CESA) listed as “Endangered”; steelhead, a species FESA-listed as
“Threatened”; tidewater gobies, a species FESA listed as “Endangered”; California red
legged frogs, a species FESA listed as “Threatened”; western pond turtles, a State
Species of Special Concern; San Francisco garter snakes, a species FESA and CESA
listed as “Endangered” and Fish and Game Code listed 9S “Fully Protected”. Other
target species are to be determined.

c) We agreed that, from our target species list we would prioritize those species listed by
FESA or CESA as threatened or endangered.

d) We acknowledge the urgency of implementing of restoration actions in Pescadero
Creek Estuary / Lagoon. We see two critical issues:
i) Immediate Issue: To prevent annual fish kill. Fish kills, including that of
federally threatened steelhead, were first reported to occur in 1995, and have
continued to be reported nearly every year since that date, coinciding with the
breaching of the sandbar at the mouth.
ii) Long-term Issue: To restore habitat. Restore the Pescadero Marsh
ecosystem to extensive seasonal (summer and fall) freshwater lagoon,
marsh, and pond habitats for the goal of increasing biological function for
target and other native species. This will also prevent the annual fish kill
associated with the breach. This issue and associated actions are urgent but
must be carried out carefully and will take more time and planning to
implement.

e) We agreed that we wanted to begin implementation of measures to address the
“immediate problem” of preventing the annual fish kills associated with the annual
breach. Of several options, we decided to pursue the “bladder dam” this year as an
“interim measure” which is to temporarily install an inflatable bladder dam in Butano
Channel near its confluence with Butano Creek. The purpose of this action is to test
whether this measure can improve water quality (dissolved oxygen concentrations)
after the breach by slowing the flow of water from the marsh during the breaching event
and thereby slow mixing in Butano Creek.
f) We prefer restoration alternatives that require no / minimal active management but will
consider management as an option if this is determined to be necessary.
g) We acknowledge that, while our agencies sometimes have different mandates, we will
work together in a collaborative process.
h) We believe that there is enough information to begin implementation of experimental
“interim measures” for the purpose of preventing the annual fish kill and also to help us
isolate variables in order to test restoration hypotheses. We do acknowledge the
existence of numerous independent variables that may make it difficult to isolate
variables and answer questions/prove hypotheses completely.

Figure 1: Pescadero Marsh Basic Conceptual Model

Pescadero is a bar-built estuary. When the bar is closed the lagoon suffers from poor water
quality, exacerbated by a heavily stratified layer of low oxygen, high temperature, brackish
water that persists throughout the closed period. Upon breaching of the sandbar, the mixing of
surface and bottom waters leads to an initial severe drop in dissolved oxygen (DO) followed by
a DO lag that persists at low tides for days to weeks. Over the last fifteen years a fish kill,
involving federally threatened steel head (Oncorhynchus mykiss), has generally occurred
during the breaching event. A study by State Parks concluded that hypoxia associated with
mixing of stratified layers is the most likely cause of the fish kill. A 1995 restoration project that
increased the tidal prism was coincident with a shift to later sandbar closure, during the driest
period of the year. Low inflows during the closed period exacerbate the poor water quality.
Pre-Project Study Plan
The proposed pre-project study is based on the recognition that waves, tides and river flow
control mouth condition; that mouth condition and river flow control water-column stratification
and residence, and, finally, that stratification and residence are primary factors in water quality.
This project will collect physical data and create a detailed conceptual model to 1) explain the
physical processes that drive mouth conditions at Pescadero 2) develop a mechanistic
understanding of the hydrodynamic conditions that arise for given mouth condition and river
flow in the lagoon 3) compare current conditions with historical conditions and 4) be a key
component in the overall assessment of Pescadero Marsh and the development of a
restoration design.
Our goal is to promote the successful restoration of Pescadero Marsh. This system is unique
from classic bar built estuaries, because of the size of the floodplain/marsh. The foremost
concern is that this bar-built west-coast estuary continues to provide valuable habitat for
anadromous salmon species (e.g., steelhead in Pescadero) and other NOAA trust resources.
This partnership of NOAA, USFWS, University of California, California State Parks, and CDFG
has two aims: (1) to develop a mechanistic understanding of the hydrodynamic conditions that
arise for given mouth condition and river flow in Pescadero lagoon or other given estuary; and
(2) to develop a mechanistic basis for morphological interventions designed to enhance or
maintain water-column habitat in bar-built estuaries.
Objectives:
• Analysis of historical data and creation of a statistical model on mouth closure based on
historical wave, tide, and river discharge measurements will be created based on a previous
study at the Russian River (preliminary model).
• Analysis of historical water quality data.
• Develop preliminary dissolved oxygen mass balance model.
• Experiment preparation including placement of a camera system near the inlet to monitor
inlet morphology and a wave/tidal height gauge offshore.
• Field measurements of wave and tide height, inflow, water quality parameters, current speed
and direction, stratification and nutrient cycling. This will allow for an analysis of the effects
of specific modifications to the tidal prism on closure habits of the lagoon inlet.
• Analysis of experimental data.
• Refine preliminary mouth conditions/ bar closure model and DO model based on field
experiment.
Deliverables:
• Report to Pescadero Marsh Working Group & hosted as USGS Open-File Report: Impacts
of sandbar formation and marsh hydrodynamics on water quality and recommendations for
restoration.
• A generalized statistical model for predicting inlet closure in bar-built estuaries along high
wave energy coasts.
• Presentations/publications:
o Hydrodynamics of sandbar formation on bar-built estuaries in California
Action Plan for the “Short Term”: Habitat Improvement of ESA Listed
Aquatic Species in Pescadero Marsh
(July 2009)
Critical Issue Description:
1) Annual Fish Kill. Generally for the last approximate 15 years, when the sandbar is
breached in late fall/winter there occurs a fish kill in the lower Butano Creek channel
near the confluence with Pescadero Creek. Variable numbers of juvenile steelhead,
crabs and other estuarine species are found dead along the shoreline of this area of the
Marsh. Water quality monitoring has shown that this generally coincides with low
dissolved oxygen and elevated high hydrogen sulfide levels in the lowered water
column. It is hypothesized that this is a result of the Butano Marsh water draining into
the main channel after the breaching occurs.
2) Late forming Sandbar/freshwater lagoon: The tidal prism has increased in
Pescadero Marsh and this has coincided with the loss of much of the habitats for
steelhead, California red-legged frog, San Francisco garter snake, and tide-water goby
(Smith 1997). Examples: California red-legged frog can only reproduce in freshwater
and is an important food source for San Francisco garter snake; tidewater goby
primarily live in backwater habitat avoiding the stronger flowing tidal water habitat;
steel head productivity is greatest in freshwater lagoons, and the greatest productivity in
Pescadero Creek Lagoon occurred during average to wet water years (Smith 1990).
Thus, the increased tidal prism is hypothesized to inhibit the normal formation of a
sandbar in late spring/summer and the formation of a large freshwater lagoon.
Formalize a relationship with Pescadero Marsh Restoration Planning Group (i.e. MOU):
This MOU could define the following: vision; goals and objectives; funding; specific agency
participation roles; timeline of project implementation; deliverables; monitoring; adaptive
management; dispute resolution.
Possible Interim Solutions:
1. “Butano Channel Water Quality Weir” (to prevent Issue 1: Annual Fish Kill).
Temporarily install inflatable bladder dam at confluence of Butano Channel and
Marsh.
DESCRIPTION:
Temporarily install an inflatable bladder dam in Butano Marsh near the confluence with
Butano Creek. The purpose of the dam is to slow the flow of water during the breaching
event from the marsh to the beach in an effort to reduce mixing and improve water quality.
This is the location where the majority of observed steel head carcasses are annually found.
JUSTIFICATION:
–The project was undertaken by NOAA Fisheries and CDFG in year 2006 and did not work
as it was designed for the following reasons: 1) the weir was installed after the bar formed
and water was 7′ deep (received environmental permits until “too late”); 2) the bladder dam
was not filled with dense / heavy enough material; 3) several bladders were cut
(presumably by large heavy debris) which reduced their integrity and allowed them to flex;
and 4) Butano Channel/Marsh was drained within 24 hrs of the sandbar breach.
–This project is still a popular concept for the locals. From a scientific and public relations
standpoint, it would be helpful to implement this project as designed to see if use of the
dam improves water quality during the breach and mitigates the fish kill.
–Ways to prevent the bladder from failing: 1) Install the bladder dam in shallow water
(before sandbar forms and at low tide); 2) Fill the bladder with heavier sand instead of the
light clayey silt; 3) Install the bladder dam horizontally with the ends flush against the banks
instead of bending the ends upstream.
PROJECT CONSTRAINTS:
–Environmental Permits are required: San Mateo County Permit; CDFG 1602; USACOE
Nationwide Permit (NOAA Fisheries and USFWS Consultations); 404 Regional Board
Permit; Coastal Commission Permit; National Marine Sanctuary Permit; NEPA; and CEQA.
–Sensitive species present include the following: coho salmon (State and federally listed as
“Endangered”); steelhead (Federally listed as “threatened”); tidewater goby (federally listed
as “threatened”); red-legged frogs (federally listed as “threatened”); San Francisco garter
snakes (State and federally listed as “Endangered” and Fish and Game Code listed as
“Fully Protected”); and western pond turtles (“species of special concern”).
–Funding AND staff time is needed for the following: repair of the bladder dams from use in
2006; environmental permits; labor for installing bladder dam; exclusionary fences; erosion
control measures; other equipment costs; water quality monitoring, and final report-writing.
MONITORING NEEDED:
Water quality, stage and transect monitoring, and fish habitat and population monitoring.
TIME FRAME: April 2009 through December 2009.
DELIVERABLE: Test whether the theory of the low water quality in the marsh is actually
causing the annual fish kill and demonstrate how this could be changed.
2. “Seasonal Restriction of North Marsh Tidal Exchange Channel” (to prevent Issue 2:
The Late Forming Sandbar and Freshwater Lagoon).
Temporarily plug large culverts that drain North Marsh/Pond directly into Pescadero
Creek.
DESCRIPTION:
Plug or dam up culverts with materials (sand bags or other materials) to determine effects
on tidal prism and sandbar formation.
JUSTIFICATION:
The sandbar now forms much later. Seasonally closing these culverts will reduce tidal
prism and action, thereby possibly allowing earlier (June-July) sandbar formation.
Additionally, earlier sandbar formation could provide substantially more backwater habitat
for tidewater gobies as well as provide freshwater habitat in North and Butano Marshes for
California red-legged frogs (and San Francisco garter snakes and western pond turtles).
PROJECT CONSTRAINTS:
–Engineers should determine if the levees are stable enough to withstand the culverts’
being plugged. It is likely that “piping” is already occurring in the levee through the rusted
culvert. Note: Even without doing this project, there is the possibility of losing this levee in
the near future if these culverts are not replaced and the levees not maintained. Some
restoration opportunities, at that point, will then be lost.
–It could take years of plugging culverts before one sees earlier sandbar formation.
–See “Environmental Permitting” and “Sensitive Species” under “A”.
–Money AND staff time is needed for the following: environmental permits; plugging of
culvert; other equipment costs; and tidal prism and water quality monitoring.
MONITROING NEEDED:
Water surface elevation, flow direction and velocity at transects to model sandbar
formation, fish habitat and population monitoring.
TIME FRAME: October 2009 through December 2010.
DELIVERABLE: Test whether the theory of the increased tidal volume exchanged is
actually causing the late forming sandbar/mouth and how this could be changed.
3. “Seasonal Restriction of North Marsh and Butano Tidal Exchange Channels” (to
prevent Issue 2: The Late Forming Sandbar and Freshwater Lagoon).
Temporarily plug large culverts that drain North Marsh/Pond directly into Pescadero
Creek and block tidal exchange into Butano Marsh.
DESCRIPTION:
Plug or dam up culverts with materials (sand bags or other materials) to determine effects
on tidal prism and sandbar formation and install (bladder) dam into Butano Marsh channel.
JUSTIFICATION:
The sandbar now forms much later. Seasonally closing these tidal channels will reduce
tidal prism and action, thereby possibly allowing earlier (June-July) sandbar formation.
Additionally, earlier sandbar formation could provide substantially more backwater habitat
for tidewater gobies as well as provide freshwater habitat in North and Butano Marshes for
California red-legged frogs (and San Francisco garter snakes and western pond turtles).
PROJECT CONSTRAINTS:
–Engineers should determine if the levees are stable enough to withstand the channels
being blocked. It is likely that “piping” is already occurring in the levee through the rusted
culverts in the North Marsh channel. Note: Even without doing this project, there is the
possibility of losing this levee in the near future if these culverts are not replaced and the
levees not maintained. Some restoration opportunities, at that point, will then be lost.
–It could take years of blocking these channels seasonally before one sees earlier sandbar
formation.
–See “Environmental Permitting” and “Sensitive Species” under “A”.
–Money AND staff time is needed for the following: environmental permits; plugging of
culvert; other equipment costs; and tidal prism and water quality monitoring.
MONITROING NEEDED:
Water surface elevation, flow direction and velocity at transects to model sandbar
formation, fish habitat and population monitoring.
TIME FRAME: October 2010 through December 2011.
DELIVERABLE: Test whether the theory of the increased tidal volume exchanged is
actually causing the late forming sandbar/mouth and how this could be changed.
4. “Manual closure and maintenance of the Sandbar” (to prevent Issue 2: The Late
Forming Sandbar and Freshwater Lagoon).
Use heavy equipment to build up an earlier forming sandbar and regulate the lagoon
level.
DESCRIPTION:
Manually buildup a sandbar in late spring/early summer and provide a means to regulate
the lagoon level.
JUSTIFICATION:
The sandbar now forms much later. Seasonally closing the sandbar/river mouth will reduce
tidal prism and action, thereby possibly allowing earlier (June-July) freshwater lagoon
formation. Additionally, earlier sandbar formation could provide substantially more
backwater habitat for tidewater gobies as well as provide freshwater habitat in North and
Butano Marshes for California red-legged frogs (and San Francisco garter snakes and
western pond turtles).
PROJECT CONSTRAINTS:
–This project would take the most planning and review by the permitting agencies and
likely would not help understanding what variables control its closure. However, it could
demonstrate the beneficial response of the freshwater aquatic organisms to a large
freshwater lagoon.
–It could take years of seasonally forming the sandbar early before one sees freshwater
marsh habitat.
–See “Environmental Permitting” and “Sensitive Species” under “A”.
–Money AND staff time is needed for the following: environmental permits; plugging of
culvert; other equipment costs; and tidal prism and water quality monitoring.
MONITROING NEEDED:
Beach and sandbar elevation, water surface elevation, water quality, fish habitat and
population monitoring.
TIME FRAME: October 2011 through December 2012.
DELIVERABLE: Test whether the theory of an earlier forming freshwater lagoon will
improve water quality conditions and support increased population use by the species of
concern.