Att_04_140P8421Q0104_KHE_Hydrology_Final_Report.pdf

HYDROLOGIC FEASIBILITY ASSESSMENT REPORT:

GIACOMINI WETLAND RESTORATION PROJECT

Prepared For:

Point Reyes National Seashore/Golden Gate National Recreation Area

Prepared by:

Kamman Hydrology & Engineering, Inc.

7 Mt. Lassen Drive, Suite B-250

San Rafael, CA 94903

(415) 491-9600

April 2008

Hydrologic and Hydraulic Feasibility Assessment Report Giacomini Wetland Restoration Project i

Services provided pursuant to this Agreement is intended for the sole use and benefit of

The National Park Service (GGNRA and Point Reyes National Seashore) No other person or entity shall be entitled to rely on the services, opinions, recommendations, plans or specifications provided pursuant to this agreement without express written consent of Kamman Hydrology & Engineering, Inc.

7 Mt. Lassen Dr., Ste. B250, San Rafael, CA 94903 ii

TABLE OF CONTENTS

Page No.

1.0 Executive Summary ……………………………………………………. 1

2.0 Introduction ……………………………………………………………. 4

2.1 Purpose and Scope of Report ………………….………………… 4

2.2 Report Organization ……………………………………………… 5

3.0 Physical Setting …………………………………………………………. 6

3.1 Site Location …………………………………..…………………. 6

3.2 Physiographic Setting …………………………..………………… 6

3.3 Project Area Topography …………………………….…………………. 7

3.4 Watershed History and Impacts ……………………..…………………. 8

3.5 Site Reclamation and Development .…………………..…………. 9

3.5.1 Giacomini Parcel Site History……………..……………… 9

3.5.2 Olema Marsh Site History …………………..……………. 12

3.5.3 Existing Levee Conditions …………………..…………… 14

3.6 Geology ………………………………………………..…………. 15

3.6.1 Regional Geology ………………………………………… 15

3.6.2 Shallow Site Stratigraphy ………………………………… 16

3.6.3 Site Soil …………………………………………..………. 18

4.0 Hydrology and Water Quality Conditions………………………………. 20

4.1 Contributing Watersheds and Internal Drainage …………………. 20

4.2 Tidal Monitoring and Influence …………………………..……… 24

4.3 Water Quality Monitoring………………………………………… 29

4.4 Bed Grain Size Analysis …………………………………………. 36

4.5 Groundwater Conditions and Quality……………………..……… 37

4.5.1 Site Groundwater Monitoring …………………………… 37

4.5.2 Point Reyes Mesa Groundwater …………………………. 39

4.5.3 Groundwater Influence on Creek Salinity…………..……. 40

5.0 Description of Restoration Alternatives ………………………………… 45

5.1 No Action ………………………………………………………… 45

5.2 Alternative A……………………………………………………… 46

5.3 Alternative B …………………………………………………..…. 47

5.4 Alternative C …………………………………………………..…. 49

5.5 Alternative D …………………………………………………..…. 51

6.0 Numerical Model Description ………………………………………..…. 52

6.1 Purpose and Scope …………………………………………….…. 52

6.2 Model Description .……………………………………………..… 52

6.3 Simulation Characteristics ……………………………………..…. 53

6.4 Hydrodynamic Model Configuration ..………………………...… 53

6.4.1 Model Network ..…………………………………………. 53

6.4.2 Initial Conditions …………………………………………. 53

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TABLE OF CONTENTS (continued) Page No.

6.4.3 Tidal Boundary Conditions: Model Calibration ………….. 53

6.4.4 Freshwater Inflows: Model Calibration ………………….. 54

6.4.5 Groundwater Sources and Withdrawals……………….….. 54

6.4.6 Channel and Floodplain Roughness Characteristics ….….. 55

6.4.7 Control Structures ………………………………………... 55

6.5 Hydrodynamic Model Calibration Results ……………………….. 56

6.6 Salinity Model Validation ………………………………………... 56

6.6.1 Modeling Assumptions …………………………………... 57

6.6.2 Salinity Calibration Results ………………………………. 57

6.6.3 Salinity Model Validation ……………………..…………. 58

7.0 Feasibility Assessment of Restoration Alternatives …………..………… 59

7.1 Flood Impact Assessment ………………………………………… 59

7.1.1 Simulated Flood Boundary Conditions …………..………. 59

7.1.2 Flood Model Simulation Results …………………………. 60

7.1.3 Fish Hatchery Creek and 1906 Drainage Flooding

Characteristics………………………………………………. 63

7.1.4 Flood Recurrence Intervals ………………………………. 64

7.2 Tidal Influence and Salinity Assessment ………………………… 64

7.2.1 Model Boundary Conditions and Assumptions ………….. 64

7.2.2 Model Simulation Results and Effect on Restoration

Design……………………………………………………... 65

7.3 Impacts on Local Water Supply Wells …………………………… 70

7.3.1 Model Boundary Conditions and Assumptions ………….. 70

7.3.2 Simulated Salinities and NMWD Wells ………………….. 71

7.4 Evaluation and Prediction of Alternative Marsh Habitats………... 75

7.5 Evaluation of Channel Stability and Evolution …………………... 78

7.5.1 Results of 2-Year Flood Simulations…………………

7.5.2 Results of Mean Tidal Month (MTM) Simulations..…

7.5.3 Long-Term Site Evolution……………………………

8.0 Restoration and Implementation Analyses ……………………………… 82

8.1 Levee Construction and Maintenance ……………………………. 82

8.2 Hydrologic Sufficiency Analysis for Tomasini Triangle

Freshwater Marsh………………...……………………………….. 83

8.2.1 Estimated Available Water Supply………………………… 84

8.2.2 Estimated Water Demands……….………………………… 86

8.2.3 Water Budget…………………….………………………… 86

8.2.4 Freshwater Wetland Design Considerations……………… 88

8.3 Sea Level Rise……………………………………………………. 88

8.4 Alternative Cost Estimates ……………………………………….. 89

8.4.1 General Assumptions ……………… ……………………. 90

8.4.2 Alternative-Specific Assumptions ………………………... 91

8.4.3 Unit Costs Associated with Project Actions ……………... 95

8.5 Recommended Additional Studies for Final Design ……………... 98 iv

Page No.

9.0 References ………………………………………………………………. 100

LIST OF TABLES

Table 4.1 Flood Frequency Estimates ………………………………………… 21 Table 4.2 Tidal Datums for NOAA Tide Gage: Tomales Bay at Inverness ….. 25 Table 4.3 Water Level Monitoring Locations and Monitoring Periods……….. 25 Table 6.1 Calibration Model Freshwater Inflow Assumptions ……….……… 55 Table 7.1 Simulated Salinity Concentrations at NMWD Wells: Average

Water Year Type…………………………...……………………….. 61 Table 7.2 Simulated Salinity Concentrations at Coast Guard Wells (Average versus Dry Water Year Type Conditions…………………………... 72 Table 7.3 Simulated Salinity Concentrations at Coast Guard Wells (Dry

Water Year-Type Conditions)………………….. …………………. 73 Table 7.4 Simulated Salinity Concentrations at Coast Guard Wells: With and

Without Lowering of Cattle Crossing Gravel Bar …………………. 74 Table 7.5 Summary of Calculated Tidal Inundation Areas and Tidal Prism

Volumes for Project Alternatives…………………………………… 76 Table 7.6 Existing and Predicted Habitat Zone Areas………………………… 77 Table 8.1 Summary of Tomasini Triangle Marsh Water Supply and Demands 85 Table 8.2 Estimated Maximum Freshwater Marsh Pond Depths……………... 87 Table 8.3 Alternatives Cost Summary………………………………………… 90

LIST OF FIGURES

(Please Note: All figures are presented at the back of the document)

Figure 3.1 Site Location Map Figure 3.2 Watersheds Draining to Project Area Figure 3.3 Existing Conditions Map Figure 3.4 USGS Topographic Map of Project Site Figure 3.5 Longitudinal Profile of Bear Valley Creek/Olema Marsh Figure 3.6 1862 National Geodetic Survey Map Figure 3.7 1961 Aerial Photograph: Olema Marsh Figure 3.8 1974 Aerial Photograph: Olema Marsh Figure 3.9 Schematic of Olema Marsh Earthen Sill above Eastern Outfall Figure 3.10 Local Geology Map Figure 3.11 Soil Boring Locations: East and West Pastures Figure 3.12 Soil Boring Locations: Lower Bear Valley Creek Figure 3.13 Grain Size Analysis Results for Soil Boring Samples Figure 4.1 Flood Frequency Curve and Annual Peak Flow Estimates: Lagunitas Creek Inflow Figure 4.2 Water Level Monitoring Locations v

Figure 4.3 Measured Versus Predicted Water Levels – Tomales Bay at Inverness Figure 4.4 Measured Water Levels – Fish Hatchery Creek (inner and outer gages) Figure 4.5 Measured Water Levels – West Pasture – Freshwater Marsh Figure 4.6 Measured Water Levels – West Pasture – Head of Old Slough Figure 4.7 Measured Water Levels – Tomales Bay, Lagunitas Creek and Mouth of Olema Creek Figure 4.8 Schematic Longitudinal Profile of Lagunitas Creek Bed Figure 4.9 Measured Water Levels Versus Creek Flow – Lagunitas Creek (at Former Diversion Intake) Figure 4.10 Measured Water Levels – Tomasini Creek (near outfall to Lagunitas Creek) Figure 4.11 Measured Water Levels – Tomasini Creek (near outfall and at Hunt Shack)

Figure 4.12 Measured Water Levels – Lagunitas & Olema Creeks, Olema Marsh, and Tomales Bay Figure 4.13 Measured Water Levels Versus Rainfall – Bear Valley Road Culvert Study Gages Figure 4.14 Surface Water Quality Monitoring Locations Figure 4.15 Measured DO and Water Temperature – Tomasini Creek Figure 4.16 Measured DO – Lagunitas Creek Figure 4.17 Measured DO – Fish Hatchery Creek Figure 4.18 Measured DO and Temperature –West Pasture Old Slough Figure 4.19 Measured DO – East Pasture Old Slough Figure 4.20 Measured DO – East Pasture Drainage Ditch Figure 4.21 Measured pH – Lagunitas Creek Figure 4.22 Measured pH – Tomasini Creek Figure 4.23 Measured pH – Fish Hatchery Creek Figure 4.24 Measured pH – East Pasture Old Slough Figure 4.25 Measured pH – West Pasture Figure 4.26 Measured Salinity – Lagunitas Creek Figure 4.27 Measured Salinity – Tomasini Creek Figure 4.28 Measured Salinity – Fish Hatchery Creek Figure 4.29 Measured Salinity – West Pasture Old Slough Figure 4.30 Measured Salinity – East Pasture Old Slough Figure 4.31 Pebble Count Grain Size Distribution – Lagunitas Creek Figure 4.32 Groundwater Monitoring Locations Figure 4.33 Results of Surface Water-Groundwater Interaction Monitoring Figure 4.34 Measured Well and Creek Chloride vs. Creek Flow: NMWD Coast Guard Wells Figure 4.35 Coast Guard Well Virtual Salinity vs. Pumping, Tides and Creek Flow Figure 5.1 No Action Alternative: Proposed Conditions Figure 5.2 Alternative A: Proposed Conditions Figure 5.3 Alternative B: Proposed Conditions Figure 5.4 Alternative C: Proposed Conditions Figure 5.5 Olema Marsh Proposed Conditions: Alternatives C and D Figure 5.6 Alternative D: Proposed Conditions vi

Figure 6.1 Numerical Model Network Figure 6.2 Numerical Model Calibration: Fish Hatchery Creek Figure 6.3 Numerical Model Calibration: Lagunitas Creek and West Pasture Old Slough Figure 6.4 Numerical Model Calibration: Tomasini Creek and Olema Creek Figure 6.5 Numerical Model Calibration: Lagunitas Creek and Olema Marsh Figure 6.6 Salinity Model Calibration: Measured Versus Simulated Figure 6.7 Creek Salinity and Water Level Monitoring Results at NMWD Coast Guard Well Figure 6.8 Simulated vs. Measured Creek Salinity at NMWD Coast Guard Wells Figure 6.9 Predicated Salinity Conc. (MTM) - Lagunitas Creek (Existing Conditions) Figure 6.10 Predicated Salinity Conc. (MTM) – Fish Hatchery Cr and Old Slough (Existing

Conditions) Figure 6.11 Predicated Salinity Conc. (MTM) - Tomasini Creek (Existing Conditions) Figure 7.1 1998 Flood and Tide Hydrographs: Numerical Model Boundary Conditions Figure 7.2 Simulated Lagunitas Creek Maximum Water Surface Elevations along Levee Road: 1998 Flood Event Figure 7.3 Simulated Peak Lagunitas Creek Water Surface Elevations along Levee Road: 1982 Flood Event Figure 7.4 Simulated Flood Inundation Areas: Existing Conditions Figure 7.5 Simulated Flood Inundation Areas: Alternative A Figure 7.6 Simulated Flood Inundation Areas: Alternative B Figure 7.7 Simulated Flood Inundation Areas: Alternative C Figure 7.8 Simulated Flood Inundation Areas: Alternative D Figure 7.9 Simulated Lagunitas Creek Water Surface Elevations along Levee Road: 2-Year Flood Event Figure 7.10 Simulated West Pasture Surface Elevations: 2-Year Flood Event Figure 7.11 Simulated Lagunitas Creek Water Surface Elevations along Levee Road: 5-Year Flood Event Figure 7.12 Simulated West Pasture Surface Elevations: 5-Year Flood Event Figure 7.13 Simulated Water Elevations along Levee Road: 10-Year Flood Figure 7.14 Simulated Lagunitas Creek Water Surface Elevations along Levee Road: 50-Year Flood Event Figure 7.15 Simulated Water Elevations along Levee Road: 100-Year Flood Event Figure 7.16 Simulated Lagunitas Creek Water Surface Elevations along Levee Road: 500-Year Flood Event Figure 7.17 Simulated Water Elevations: 10-Year Flood – West Pasture Figure 7.18 Simulated West Pasture Surface Elevations: 50-Year Flood Event Figure 7.19 Simulated West Pasture Surface Elevations: 100-Year Flood Event Figure 7.20 Simulated West Pasture Surface Elevations: 500-Year Flood Event Figure 7.21 Change in Flood Recurrence Interval for Overbank Flooding Figure 7.22 Predicted Hourly Water Levels for Mean Tidal Month: Tomales Bay at Inverness Figure 7.23 Predicted Water Levels (Mean Tidal Month) – Central East Pasture Figure 7.24 Predicted Salinity Concentrations for Alternatives – Central East Pasture Figure 7.25 Predicted Water Levels for Alternative D – Tomasini Triangle Figure 7.26 Predicted Salinity Concentrations for Alternative D – Tomasini Triangle vii

Figure 7.27 Predicted Water Levels (Mean Tidal Month) – Central West Pasture Figure 7.28 Predicted Salinity Concentrations for Alternatives – Central West Pasture Figure 7.29 Predicted Water Levels (Mean Tidal Month) – Olema Marsh Figure 7.30 Predicted Salinity Concentrations for Alternatives – Olema Marsh Figure 7.31 Predicted Water Levels (Mean Tidal Month) – Lagunitas Creek North of Cattle Crossing Figure 7.32 Predicted Salinity Concentrations for Alternatives – Lagunitas Creek North of Cattle Crossing Figure 7.33 Predicted Water Levels (Mean Tidal Month) – Lagunitas Creek at Olema Creek Mouth Figure 7.34 Predicted Salinity Concentrations for Alternatives – Lagunitas Creek near Olema Creek Mouth Figure 7.35 Predicted Water Levels (Mean Tidal Month) – Tomasini Creek near Outfall Figure 7.36 Predicted Salinity Concentrations for Alternatives - Tomasini Creek near Outfall Figure 7.37 Predicted Creek Salinity Concentrations at NMWD Coast Guard Well:

Average Year-Type Figure 7.38 Predicted Creek Salinity Concentrations at NMWD Coast Guard Well:

Dry Year-Type Figure 7.39 Predicted Creek Salinity Concentrations at NMWD Wells for Lower Cattle Xing

Gravel Bar – Alternative D Figure 7.40 Predicated Habitat Zones: Existing Conditions Figure 7.41 Predicated Habitat Zones: Alternative A Figure 7.42 Predicated Habitat Zones: Alternative B Figure 7.43 Predicated Habitat Zones: Alternative C Figure 7.44 Predicated Habitat Zones: Alternative D Figure 7.45 Simulated Bed Shear Stress – Lagunitas Creek Channel – 2-Year Flood Figure 7.46 Simulated Bed Shear Stress – East Pasture Floodplain – 2-Year Flood Figure 7.47 Simulated Bed Shear Stress – West Pasture Floodplain – 2-Year Flood Figure 7.48 Simulated Bed Shear Stress – Olema Marsh – 2-Year Flood Figure 7.49 Simulated Maximum Velocities – Lagunitas Creek Channel – Mean Tidal Month

Conditions Figure 7.50 Simulated Maximum Velocities – East Pasture – Mean Tidal Month Conditions Figure 7.51 Simulated Maximum Velocities – West Pasture – Mean Tidal Month Conditions Figure 7.52 Simulated Maximum Velocities – Olema Marsh – Mean Tidal Month Conditions Figure 8.1 Tomasini Triangle Freshwater Wetland – Location and Contributing Drainage

Area

LIST OF APPENDICES

Appendix A: Logs of Soil Borings Appendix B: Soil Testing Laboratory Reports: Grain Size and Organic Content Appendix C: Project Implementation Cost Estimate Tables

1.0 EXECUTIVE SUMMARY

The National Park Service’s Point Reyes National Seashore and Golden Gate National Recreation Area are proposing to restore and enhance the Giacomini Dairy Ranch and adjacent Olema Marsh, located at the south end of Tomales Bay near Point Reyes Station, California. The objective of this wetland restoration project is to restore natural hydrologic and geomorphic processes in an effort to restore natural ecological processes and enhance habitat for special-status species. Much if not all of the project area was significantly altered by human development and site reclamation by diking and draining preexisting tidal wetlands. Levee systems have also been constructed to reduce overbank flooding from Lagunitas and Tomasini Creeks. As part of the restoration planning and design effort, the National Park Service retained Kamman Hydrology & Engineering, Inc. (KHE) to complete a series of hydrologic monitoring investigations and modeling assessments with the goal of evaluating the hydrologic/hydraulic feasibility of proposed restoration alternatives. The numerical model was also used to assist in refining restoration designs.

The hydrology-based feasibility analyses consisted of conducting numerous field investigations to characterize and quantify existing site hydrologic and geomorphic conditions. Specific studies KHE conducted include monitoring the extent and magnitude of tidal influence throughout the site; conducting a number of topographic and hydrographic surveys; characterizing shallow subsurface stratigraphy and monitoring shallow groundwater conditions; and monitoring surface and groundwater quality. Significant findings from field-based investigations include:

• A site topographic survey suggests that most of the site is at or above the intertidal elevation.

• The site is underlain by a mixture of creek, delta, and estuary deposits, but has not significantly subsided because of these recent agricultural practices.

• Tide gates on Fish Hatchery and Tomasini Creeks are partially open, permitting significant, but muted, tidal exchange to upstream sections of these creeks.

• Tidal monitoring results indicate there is little tidal damping of high tides in distal upstream reaches unaltered by control structures, but creek channel bars act as grade control structures, truncating lower tidal range to varying degrees.

• Water quality monitoring results indicates the site waterways display seasonal shifts and concentration variability in major water quality parameters (e.g., salinity) because of a balance between the varying degrees of freshwater inflow and tidal influence.

• Channel bed sampling and numerical modeling results indicate Lagunitas Creek transports a large volume of material including coarse gravel size through the project reach during frequent (2-year recurrence) floods. The channel appears to be generally stable, and there are no signs of ongoing incision or deposition.

• Shallow groundwater conditions persist across the site. Groundwater is generally brackish except along the western and eastern margins of the project site where higher inflows from water-bearing valley-margin deposits maintain freshwater conditions at the surface and in the shallow groundwater.

• Shallow groundwater table gradient beneath the East Pasture is such that groundwater flow is, in general, to the north-northwest, away from the mouth of Lagunitas Creek and the North Marin Water District water supply wells.

• Olema Marsh has evolved as vegetation-choked freshwater marsh complex due to sediment infilling of outlet culverts. As a result, ponding has expanded with the static marsh water level rising over 6-feet in elevation since 1990. Subsurface investigations within/around the marsh indicate bed materials consist of peat, not clastic materials previously believed to be filling the marsh.

• The results of field investigations also provided data for the development and calibration of an integrated one-dimensional flow-salinity model, used to evaluate the performance, feasibility and flood impacts of proposed alternatives. Final project alternative design also utilized the numerical model to predict the type and sustainability of various habitat types and sensitive species including: riparian; salt marsh; fluvial; freshwater marsh; tidewater goby;

California red-legged frog; and anadromous fish such as coho and steelhead. Highlights of the alternative feasibility assessments include:

• Model simulation results indicate that a large majority of the Project Area will be subject to tidal action.

• Proposed restoration alternatives represent a continuum between No Project and full tidal restoration to the extent possible given the dominance of above-intertidal grades at the site.

• The numerical flow and salinity model accurately simulates water levels and salinity concentrations throughout the project area, within Olema Marsh/Lower Bear Valley Creek, and in Lagunitas Creek up to and through the NMWD wells.

• Relative to the No Action alternative, hydrodynamic modeling of alternatives indicate that each Action Alternative effectively reduces the 2- through 500-year peak flood level along Levee Road. In contrast, modeling results indicate increased flood water levels in portions of the West Pasture adjacent to the property in-holdings for the 2- through 500-year floods, but not to levels that threaten structures. Existing homes reside at the highest project elevations on the apex of alluvial fans. Current flooding hazards to these homes arise from sediment and debris-laden flows from Inverness Ridge tributaries that outfall onto the same alluvial fans.

• Simulation of summer low-flow, tide-dominated conditions indicate that the West Pasture freshwater marshes will be impacted by the introduction of saline waters under alternatives that restore tidal exchange to these areas. A large site exists in the East Pasture where comparable freshwater marsh may be created to mitigate for potential impacts.

• Restoration actions proposed in Olema Marsh will drain the freshwater pond/marsh complex and reintroduce tidal and brackish water influences.

• Model simulations indicate that restored sections of slough channels in the West and East

Pastures that receive spring/seep inflow will generate important Tidewater goby habitat conditions similar to those that currently exist(and will remain) in Tomasini Creek.

• The high salinities of shallow groundwater measured in the Tomasini Triangle area may complicate the creation of California red-legged frog breeding habitat. Similar subsurface conditions exist in the West Pasture and have not precluded the formation of overlying freshwater marsh conditions.

• Reduced Lagunitas Creek salinity concentrations were simulated in association with the termination of pumping from the NMWD Downey well under the No Action alternative.

These waters will remain in the creek.

• Implementation of all Action Alternatives will not adversely impact salinity concentrations near the NMWD wells.

• Given the cumulative effects associated with project implementation, Action Alternatives, as proposed, will restore (to varying degrees) natural hydrologic and geomorphic processes that reflect a balance of fluvial and tidal disturbance and variability. In turn, these changes will lead to a diverse mosaic of self-sustaining conditions that will enhance or restore riparian, avian, salt marsh, and aquatic species habitat. Potential impacts to California red-legged frog habitat in the West Pasture as a result of implementation of Alternatives B through D will be mitigated through creation of freshwater marsh in the East Pasture. It is anticipated that increases in riparian corridor width and floodplain diversity will also provide the red-legged frog with suitable habitat alternatives.

2.0 INTRODUCTION

The Point Reyes National Seashore (Seashore) and Golden Gate National Recreation Area (GGNRA) are proposing to restore and enhance the Giacomini dairy ranch and adjoining freshwater Olema Marsh as part of the Giacomini Wetland Restoration Project near Point Reyes Station, California. The primary objectives of the Giacomini wetland restoration project are:

1) To restore natural tidal and freshwater hydrologic and geomorphic processes in order to promote restoration of natural ecological processes and (to the extent possible) enhance habitat for other special-status species;

2) To avoid increases of flood risks to adjacent properties and saltwater intrusion into area wells above currently existing levels; and,

3) To accommodate the potential for land- and water-based recreational opportunities as long as they don’t conflict with restoration goals and objectives.

The Seashore retained Kamman Hydrology & Engineering, Inc. (KHE) to provide hydrology and hydraulics technical support in the design and evaluation of proposed project alternatives. Five project alternatives were developed and evaluated, along with existing site conditions, as part of this effort: four Action Alternatives and a “No Action” alternative as required by the National Environmental Policy Act (NEPA) and California Environmental Quality Act (CEQA). These restoration alternatives represent a continuum between “No Project” and restoring “Maximum Restoration” conditions.

2.1 Purpose and Scope of Report

The purpose of this report is to document the results of hydrology and hydraulic studies completed by KHE in the design and assessment of restoration alternatives. The hydrologic, geomorphic and hydraulic analyses completed includes: reviewing background materials;

designing and implementing hydrology and geomorphic field investigations and topographic surveys; contracting and managing a geotechnical field investigation; and developing a hydrodynamic and salinity model for use in designing and evaluating proposed restoration alternatives. The two primary goals of the hydrologic evaluation are: 1) to provide a meaningful comparison of the relative magnitude/extent of wetland restoration under each alternative, and 2) to evaluate the impacts of proposed restoration actions on flood risks and salinity structure within the Lagunitas Creek corridor.

KHE also worked closely with Seashore staff in addressing other objectives, such as: integrating restoration planning for the Giacomini project with fish passage improvement and ecological enhancement efforts on lower Bear Valley Creek and Olema Marsh; providing public access and recreational opportunities; minimizing long-term maintenance requirements; and developing a cost-effective restoration plan. Other impacts KHE evaluated included: impacts on local water quality; disturbance of existing habitats and sensitive species; changes to land use or public access; flooding; mobilization of contaminants1 or other impacts to water quality; and other key issues as required under NEPA/CEQA.

This study builds on previous restoration planning efforts. This report does not present historical information or results of previous study findings unless pertinent to a discussion of results from this study. This report does not address public access plans or proposed trail alignments, which

1 No contaminants of concern were found or subsequently addressed as part of this study.

are an integral part of the restoration planning effort. Reports prepared by LandPeople (2005) and KHE et al. (2004) provide descriptions and technical evaluations of proposed public access alignments.

2.2 Report Organization

This report consists of nine sections described briefly below.

• Section 1.0, “Executive Summary” summarizes the goals and findings of the study;

• Section 2.0, “Introduction” summarizes the purpose and scope of the study;

• Section 3.0, “Physical Setting” describes the physical site setting and reclamation history;

• Section 4.0, “Hydrology and Water Quality Conditions” describes the hydrologic setting and results of field monitoring programs;

• Section 5.0, “Description of Restoration Alternatives” describes the objectives and components of proposed project alternatives;

• Section 6.0, “Numerical Model Description” presents the data and assumptions used to develop, calibrate and validate the flow and salinity models utilized for alternatives design and evaluation;

• Section 7.0, “Feasibility Assessment of Restoration Alternatives” presents the results of hydraulic and geomorphic assessments completed to evaluate and refine alternative designs, and characterize the associated habitats and flood risks;

• Section 8.0, “Restoration Implementation Analyses” summarizes the results of studies completed to assist in construction planning and evaluation; and

• Section 9.0, “References” presents an alphabetical list of documents cited throughout the report.

3.0 PHYSICAL SETTING

3.1 Site Location

The Giacomini Project Wetland Restoration Site (the Site) lies at the south end of Tomales Bay, located approximately 30-miles northwest of downtown San Francisco in Western Marin County, California. The Giacomini parcel site area is approximately 550-acres in size (East Pasture is 350-acres and West Pasture is 200-acres), and the Olema Marsh project area (including County lands between Levee Road and Lagunitas Creek) are 78-acres (see Figure 3.1). The Giacomini property is divided into the Eastern and Western Pastures by Lagunitas Creek. The town of Point Reyes Station boarders the eastern side of the project site while Inverness Station is found along the west side of the site. The towns of Inverness and Olema lie several miles to the northwest and southeast of the site respectively.

The northern border of Olema Marsh is defined by an east-west alignment Sir Francis Drake Boulevard (locally referred to as Levee Road). At the northwest corner of Olema Marsh. Levee Road turns north and boarders the western side of the West Pasture. The western margin of Olema Marsh is bordered by Bear Valley Road. There are a number of privately owned parcels immediately adjoining the project site that are of special concern to the project, including.

Specifically, the Gradjanski, Kostelic and Lucchesi properties lie east of Sir Francis Drake extending into the main body of the West Pasture and approximately 12- parcels located along Levee Road between Olema Marsh and the intersection with Highway 1 (see Figure 3.1). The Giacomini Dairy Farm is located in the southeast corner of the Site.

3.2 Physiographic Setting

The Site occupies the upper region of the Lagunitas Creek delta (historically known as the Papermill Creek delta), which is located at the south end of Tomales Bay (Figure 3.1). Tomales Bay is a relatively shallow estuary that occupies a long, linear, submerged valley along the northwest-trending San Andreas Fault zone. The Bay is bordered by the relatively rugged topography of Inverness Ridge on the southwest and Bolinas Ridge on the northeast. Eight separate watersheds with a cumulative drainage area of 105 square miles outfall to the Project site (see Figure 3.2). The watersheds draining to the site, from largest to smallest, include: 1) Lagunitas Creek (83.1-square miles); 2) Olema Creek (14.7-square miles); 3) Bear Valley Creek (4.1-square miles); 4) Tomasini Creek (3.3-square miles); 5) Fish Hatchery Creek (0.9-square miles); 6) Haggerty Gulch (0.7-square miles); 7) the Creek 2 or 1906 drainage (0.2-square miles);

and the 8) the unnamed tributary (less than 0.1-square miles). Lagunitas Creek flows in an east west alignment between its entrance into the project area at the Highway 1 Bridge (locally referred to as Green Bridge) and the southwest corner of the West Pasture (see existing condition Site map, Figure 3.3). At this point, the Creek makes a 90-degree turn to the north, flowing to its outfall into Tomales Bay. The deep scour hole that has developed at this bend has been named White House Pool. Olema and Bear Valley creeks, which are major tributaries of Lagunitas Creek, join it upstream of White House Pool. Olema Marsh actually occupies the lower-most section of Bear Valley Creek. Tomasini Creek drains the ridge and mesa lying to the east of the project site. The small, steep watersheds of (from south to north) Haggarty Gulch, Fish Hatchery Creek, Creek 2, and unnamed creek drain off the eastern flank of Inverness Ridge.

The reach of Lagunitas Creek that flows through the Site is confined by earthen levees along much of its length through the project site. An earthen levee exists along the entire right bank of Lagunitas Creek bordering the East Pasture. A levee also borders the West Pasture along Lagunitas Creek from a point just north of White House Pool, where the upstream end of the West Pasture levee merges with Levee Road, to the northern project boundary. Here, the earthen levee that borders the north perimeter of the West Pasture is named the North Levee. The East

Pasture is also bordered on the east below the Point Reyes Mesa by an earthen levee (hereafter referred to as the Tomasini Creek levee). The Tomasini Creek levee defines the left bank of the creek, which has been relocated from the East Pasture to flow along the eastern perimeter of the Site. The east bank of Tomasini Creek is marked by the former Union Pacific railroad grade. The west side of the Site is bordered by roadway embankment fills underlying Sir Francis Drake Highway.

3.3 Project Area Topography

Giacomini Parcel Figure 3.4 presents a topographic map with adjacent wetland areas prepared by the U.S.

Geological Survey (USGS, 2003). The vertical datum of the map is the North American Vertical Datum of 1988 (NAVD88), which at the site is essentially equivalent to the MLLW tidal datum and 2.61-feet below the National Geodetic Vertical Datum of 1929 (NGVD29). Throughout this report, unless otherwise indicated, all elevations are expressed relative to the NAVD88 datum.

The map indicates that the majority of the active pasturelands are relatively flat, having an average elevation of 4-feet NAVD88 in the East Pasture and 5-feet NAVD88 in the West Pasture.

In general, the East Pasture is highest along the south margin (11-feet NAVD88) and slopes down to the average pasture elevation of 4-feet approximately at a distance of approximately one-quarter of the pasture length to the north. This sloping surface is part of two similar geomorphic features, one being the face of a natural alluvial fan building out onto the historic marsh plain from the mouth of Lagunitas Creek and the other being a wedge of fine grained sediment splayed onto the East Pasture through a low spot in the levee during repeated flooding. The East Pasture is essentially flat over its northern three-quarters.

The east half of the West Pasture (located immediately west of the Lagunitas Creek levee) slopes gently and evenly from approximately 8-feet NAVD88 at the south end to 5-feet NAVD near the North Levee. Ground surface elevations along the western margin of the West Pasture and along Sir Francis Drake Road range from 14-feet NAVD88 (at the south end) to 21-feet NAVD88 (at the north end). Topography is heavily influenced by alluvial fans that have formed at the mouths of several creeks that discharge onto the West Pasture along the base of Inverness Ridge. Several residential inholdings are located along the west margin of the West Pasture (Lucchesi, Kostelic, and Gradjanski properties labeled on Figure 3.3) on the apex of the alluvial fans that form at the base of Fish Hatchery Creek and “Creek 2/1906” drainages. Elsewhere within the project area, the highest ground elevations (up to about 30-feet NAVD88) occur at the Giacomini Dairy Farm in the southeast corner of the site. The lowest elevations on the map (about 0-feet NAVD988) correspond to bed elevations in interior drainage channels in both the East and West Pastures.

The West Pasture levee top averages about 12-feet in elevation at the south end, and 10-feet at its intersection with the North Levee. Its worth noting that the elevation of the Lucchesi, Kostelic, and Gradjanski houses are at elevations ranging from approximately 14- to 17-feet; 2- to 5-feet higher than the West Pasture levee crest elevations. The North Levee has an average elevation of approximately 10-feet. Along this same span, the East Pasture levee top is typically about 2-feet lower in elevation than the West Pasture levee. Concrete spillways approximately 180-feet long with crest elevations around 7.5-feet NAVD88 occur at the north end of both the East and West Pastures. These structures are designed to drain seasonal floodwaters from each pasture.

The East Pasture levee is actually absent upstream from between White House Pool and the approximate location of the former summer dam (see Figure 3.3). However, the top of bank elevation along this levee-less stretch is between 11- and 12-feet in elevation. Upstream of the former summer dam, the East Pasture levee crest is between 14- and 17-feet in elevation. Based on the USGS (2003) topographic map, the elevations of the levees surrounding the West Pasture are lower than the ground surface elevations near the homes adjacent to the western margin of the Site. Similarly, the elevations of the levees surrounding the East Pasture are lower than the elevations at the Giacomini Dairy Farm. Therefore, the levees currently do not provide flood protection for any of these structures.

Lower Bear Valley Creek/Olema Marsh The eastern boundary of lower Bear Valley Creek/Olema Marsh is marked by the medial ridge that occupies the center of the San Andreas Fault valley and rises to an elevation of over 120-feet.

Bear Valley Creek is bounded to the west by the Inverness Ridge. Topographic surveys were completed in Olema Marsh in February 2004 and along Bear Valley Creek between Park headquarters and Olema Marsh in January and November 2005. A representative longitudinal profile of marsh and channel (bed) elevations along Bear Valley Creek between its confluence with Lagunitas Creek and Park headquarters is provided in Figure 3.5. The central portion of Olema Marsh lies at an elevation between 4- and 6-feet NAVD88. Again, the existing outfall channel borders the eastern edge of Olema Marsh. This channel becomes better defined and functional the closer it gets to the box culvert outfall. A discernable channel was only recognizable over the length identified in Figure 3.XX - south of this trace, no distinct channel or perceptible flow was observed over the 2004/05 monitoring period. Where discernable, the channel is separated from the main ponded water body of Olema Marsh by a low berm, likely constructed with dredge spoils from channel/ditch creation and/or maintenance. The height and width of the berm increases to the north and a representative cross-sectional profile through the channel is provided in Figure 3.XX. Rills and scour marks were observed across the berm at several locations at the north end of the marsh, likely created by water spilling from the main pond area into the outfall channel during high water events. The capacity of the outflow channel is limited by a narrow and shallow profile at the south end. In addition, a thick accumulation of tules, cattails and willows in and around the channel (especially the southern end) impede and slow the movement of water into and through the channel. Hydraulic modeling results further characterize the existing flow conditions through Olema Marsh indicating flood and high fish passage flows well below 1.0-fps through the upper and central portion of the marsh.

Upstream of Bear Valley Road, the existing marshplain starts at an elevation of approximately 6-feet (NAVD88) and gradually slopes upward for a distance of 1600-feet to an elevation of approximately 9-feet NAVD88 (see Figure 3.5). Upstream of this point, the valley bottom steepens and the creek occupies a well-developed channel within a broad floodplain.

There are no levees on the south side of Lagunitas Creek between Green Bridge and White House pool to protect Levee Road or existing residences from flooding. As its name implies, Levee Road acts as a levee itself. The crest of Levee road is concave in shape, with roadway high points of 12.5- and 13.2-feet NAVD88 at the east and west ends where it borders Olema Marsh and falling to 11.6-feet midway in between. Similarly, Bear Valley Road is an earthen berm with 60-foot top-width, bisecting a lower portion of Bear Valley Creek and bordering the south- and western margins of Olema Marsh (see Figure 3.1). Crest elevation of Bear Valley Road range from 15.6- to 14.6-feet NAVD88 and are approximately 7- to 8-feet above the marsh plain surfaces in lower Bear Valley Creek and Olema Marshes.

3.4 Watershed History and Impacts

Over the past 150 years, there have been significant human activities and land use changes in area watersheds that have been significantly altered hydrologic and geomorphic conditions at the Site.

A brief summary of these changes is presented below. For more detailed discussions the reader is referred to PWA (1993), Niemi and Hall (1996), and California EPA, State Water Resources Control Board (1995).

With the advent of European settlement, a number of activities occurred within the watershed prior to 1918 that led to increased sedimentation and northward progradation of the Lagunitas Creek delta into Tomales Bay. The settling and development of large sheep and dairy ranches on the Point Reyes Peninsula denuded vegetation and introduced non-native grasses and weeds, changing the vegetative cover of the land. Intense logging of redwood trees was initiated in the Lagunitas Creek basin (Samuel Taylor built a paper processing mill on Lagunitas Creek in the 1860’s) as was logging of Douglas fir for cordwood in the Olema Creek basin (Niemi and Hall, 1996). The North Pacific Coast Railroad track was completed along the east shore of Tomales Bay between 1873-74 and Sir Francis Drake Boulevard was built across the mouth of Bear Valley Creek sometime after 1892 (Ibid). All of these activities contributed to the destabilization of hill slopes and stream channels, accelerating soil erosion, salutation, and northwest progradation of the Lagunitas Creek delta.

Water development was initiated in the Lagunitas Creek watershed with the construction of Lake Lagunitas in 1873 (350 acre-feet [AF] of capacity). This was followed by damming to form Phoenix Lake in 1905 (411 AF of capacity). Beginning in 1875, several water companies were created and provided water to the rural communities of Point Reyes Station, Inverness Park, and Olema (SWRCB, 1995). Reservoir construction continued through 1982 with the following facilities:

• Alpine Lake (1918) with a capacity of 3069 AF;

• Alpine Lake expansion to 4600 AF in 1924;

• Alpine Lake expansion to 8900 AF in 1941;

• Kent Lake (1953) with a capacity of 16,050 AF;

• Nicasio Reservoir (1960) with a capacity of 22,430 AF;

• Soulajoule Reservoir (1980) with a capacity of 10,570 AF; and

• Kent Lake expansion to 32,900 AF in 1982.

Between 1862 and 1954, deposition at the head of Tomales Bay caused the delta to prograde almost 1.2 miles to the northwest, with over half of this expansion occurring between 1862 and 1918 (PWA, 1993). After 1954, the rate of delta progradation decreased significantly. The construction of Kent Lake (in 1954) and Nicasio Reservoir (in 1959) in the Lagunitas Creek watershed trapped and reduced sediment input into Lagunitas Creek (PWA, 1993; Niemi and Hall, 1996). Erosion and downstream sediment delivery rates also decreased after the turn of the century as logged slopes revegetated. This human-induced cycle of increase and subsequent return to preexisting erosion and sediment delivery rates to the project site is well documented by a number of sediment studies as summarized in Niemi and Hall (1996). However, episodic flooding, such as that which occurred during the January 1982, has deposited significant amounts of sediment in Tomales Bay (Anima and others, 1989).

3.5 Site Reclamation and Development

3.5.01 Giacomini Parcel Site History

Land Reclamation The expansion of the Lagunitas Creek delta and associated expansion of salt marsh encouraged the reclamation and conversion of approximately 550-acres of former salt marsh to pasturelands for daily cattle grazing and hay farming. On October 28, 2003, Mr. Greg Kamman (KHE) and Mr. Todd Crampton and Mr. Mike Traubenik of Geomatrix Consultants interviewed Mr. Richard Giacomini. The purpose of the interview was to obtain information regarding the site and levee construction history as well as an interpretation regarding the historic and current performance of the Site levees. Mr. Giacomini provided invaluable information regarding the history of the levees and other aspects of the Site. The parcel site histories presented below attempts to accurately reflect the information contributed by Mr. Giacomini. To aid in this summary, refer to Figure 3.3, which depicts existing site conditions and structures referenced throughout this section of the report.

In his testimony before the SWRCB (1995) at the Lagunitas Creek water rights hearing, Waldo Giacomini (Richard’s father) stated that the Giacomini land was originally “tidal marsh” and at high tide, saltwater would cover most of the property. According to Mr. Richard Giacomini, his father constructed the first Site levees adjacent to Lagunitas Creek during the mid-1940s. In total, 1.5-miles of levee were constructed along Lagunitas Creek (SWRCB, 1995). The levees were constructed entirely with “in-place” materials found on Site. The materials used to construct the levees along Lagunitas Creek were excavated from the creek banks and bed and mounded on the ground surface next to the channel. Bank material was preferred to creek bed material, thus levees were “set back” from the creek to obtain more bank material for construction. Originally, the East Pasture levee extended along Lagunitas Creek between White House Pool and the former Summer Dam with a crest elevation similar to adjacent sections in the East Pasture. However, after repeated damage from flooding, this levee was left lower to encourage the onset of flooding in the East Pasture at this location. Currently, flooding approximately every 4- to 5- years overtops this non-leveed portion of the East Pasture levee. As a result, sediment deposited during floods has preferentially accumulated at this location in the east pasture.

The East Pasture levee also originally bordered the creek all the way upstream from the former Summer Dam location to Green Bridge, but “was blown out frequently”. This reach of levee was relocated further north to its current position after the intervening triangular portion of property lying between the current levee and Lagunitas Creek was sold to the State Lands Commission.

Further to the north, the straight north-south aligned segment of Lagunitas Creek near the interior pump-house drain outfall was excavated by the Giacominis to obtain material to build the adjacent levee in the East Pasture. Life-long local resident Rich Lucchesi recalls Waldo Giacomini contracting a local gentleman with a drag line to dredge Lagunitas Creek channel from the former summer dam site downstream through White House Pool on a near annual basis (Rich Lucchesi, National Park Service, personal communication, January, 2006). Rich also recalls the Giaomini Levees requiring frequent maintenance and repair.

The materials used to construct the North and Tomasini Creek levees were excavated from the marsh plains and/or slough channels that existed at those locations, and mounded on the adjacent ground surface. The channel lying north of the North Levee is the borrow pit from where material was extracted to construct the North Levee. None of the levee fill was compacted during construction, other than wheel-rolling/tracking with the available equipment. In the late 1940s, two concrete spillways were constructed in the levees at the north end of each pasture (see Figure 3.3). Both were “designed” with a crest elevation equivalent to a 6.5-foot high tide. Based on topographic surveys completed in 2003, these 180-foot long weirs have crest elevations at approximately 7.5-feet NAVD88.

The Tomasini Creek levee was constructed sometime between 1955 and 1960. This levee was constructed to divert Tomasini Creek out of its natural channel alignment into and through the East Pasture. Mr. Giacomini indicated that Tomasini Creek is a flashy system, and high intensity, short-duration storms will cause flooding, especially during high tides. Erosion and breaches in this levee are most prevalent on the bend, just north of the Hunt Shack. One-way floodgates were installed at the mouth of Tomasini Creek, and at the mouth of Fish Hatchery Creek in the West Pasture (see Figure3.3).

Review of available historic aerial photographs from 1942 and 1943 indicate that attempts to redirect Tomasini Creek in a southward direction, along the base of the Mesa below the Giacomini dairy barns and manure piles/ponds, through the current State Lands parcel to an outfall point into Lagunitas Creek opposite of the mouth to Olema Creek. This alignment has not been verified by with the Giacomini family. The 1942 aerial image also indicates the presence of an alluvial fan on the East Pasture marsh plain at the mouth of Tomasini Creek. There is no indication that Tomasini Creek occupies the current alignment along the eastern margin of the East Pasture in either the 1942 or the 1943 aerial photographs.

A significant portion of the East Pasture levee upstream of the water diversion structure in Lagunitas Creek (riprap reach indicated on Figure 3.3) was partially “washed out” by the severe winter floods of 1981-82. Mr. Giacomini noted that every levee on the property was under water during the 1982 floods, and this was the only time he had ever witnessed this magnitude of flooding at the Site. In 1982, the COE armored the right bank of Lagunitas Creek at this location with riprap in the area of the flood damage. This work was followed by levee repair by the Giacominis, who imported approximately 200- to 300-yards of fill material to “shore up” the levee at this location. The materials used for levee reconstruction were obtained from a Caltrans landslide repair project on Black Mountain (located east of the Site).

The Site levees have been maintained and/or repaired periodically on an as-needed basis. Mr.

Giacomini indicated that the last flood-induced levee breach was between 5- to 7-years prior to the date of the interview. Levee repairs typically involved excavating materials from the adjacent creek bottoms and placing it atop the existing levees. ”Weak spots” or erosion-prone areas in the levees as noted by Mr. Giacomini exist along the Tomasini Creek levee near the Hunt Shack (mentioned above), and along the northern end of the West Pasture levee. Most of the levee along the West Pasture was rebuilt after the 1982 floods. Seeps and animal burrows (esp. badgers and muskrat) have both historically contributed to levee damage requiring maintenance/repairs.

Along the west-northwest side of the West Pasture, Mr. Giacomini noted that the drainage channels/ditches entering from the Inverness Ridge deposit “tons” of sediment that requires removal and maintenance on a regular basis.