NOVATO CREEK HYDRAULIC STUDY ANALYSIS OF ALTERNATIVES

PREPARED FOR:

County of Marin Department of Public Works

BY:

Kamman Hydrology & Engineering, Inc. 7 MT. LASSEN DRIVE, SUITE B250 San Rafael, CA 94903 (415) 491-9600

IN ASSOCIATION WITH:

WRECO 1243 Alpine Rd, Suite 108 Walnut Creek, CA 94596

June 2016

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Services provided pursuant to this Agreement are intended for planning purposes for the The Marin County Department of Public Works

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

TABLE OF CONTENTS Page No.

1 EXECUTIVE SUMMARY ...... ES‐1 1.1 Summary of Study Alternatives: ...... ES‐3 Short Term Alternative: ...... ES‐4 Medium Term Alternative: ...... ES‐10 Long Term Alternative: ...... ES‐14 1.2 Alternatives Analysis ...... ES‐18 1.3 General Flood Study Findings ...... ES‐22 1.4 Alternative Analysis Conclusions ...... ES‐26 Short Term Elements: ...... ES‐26 Medium Term Elements: ...... ES‐27 Long Term Elements: ...... ES‐27 1.5 Sea Level Rise Impacts ...... ES‐28 1.6 Recommendations ...... ES‐28 Priorities for Next Phases of Work ...... ES‐28 Additional Projects: ...... ES‐28 ...... ES‐29 2 INTRODUCTION ...... 2‐1 2.1 Physical Setting ...... 2‐3 2.2 Approach ...... 2‐5 3 STUDY ELEMENTS AND RANKING ...... 3‐1 3.1 Project Elements Determination ...... 3‐1 3.2 Project Elements Evaluation: The Criteria Development and Ranking Process ...... 3‐8 4 STUDY ALTERNATIVES ...... 4‐1 4.0 Study Alternatives Overview: ...... 4‐1 4.1 Short Term Alternative Elements: ...... 4‐2 4.2 Medium Term Alternative: ...... 4‐11 4.3 Long Term Alternative Elements: ...... 4‐19 5 ALTERNATIVES ANALYSIS ...... 5‐1 5.1 Alternatives Analysis of Design Storms ...... 5‐2 Medium Term Alternative Analysis Summary ...... 5‐19 Long Term Alternative Analysis ...... 5‐30 5.2 Comparison of Short Medium and Long Term Altenatives ...... 5‐42 5.3 Alternatives Analysis of Sea Level Rise Impacts ...... 5‐55 5.4 Alternative Analysis of Mid‐Tide Scenarios ...... 5‐56 6 NPW STUDY CONCLUSIONS ...... 6‐1 6.1 General Findings: ...... 6‐1 6.2 Alternatives Analysis Conclusions ...... 6‐4 Short Term Alternative Elements: ...... 6‐4 Medium Term Elements: ...... 6‐5 i‐2

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Long Term Elements: ...... 6‐5 6.3 Recommendations ...... 6‐6 Recommendations for Next Phases of Work ...... 6‐6 Additional Project Elements: ...... 6‐6 Concepts Recommended for Additional Study: ...... 6‐6

LIST OF APPENDICES

Attachment A: Participating Stakeholders Attachment B: Study Elements Attachment C: Element Ranking Criteria Attachment D: Creek Modeling Results Attachment E: Bayland Modeling Results

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

LIST OF FIGURES Page No.

Figure ES‐1: Short Term Alternative Elements ...... ES‐6 Figure ES‐2: Q50 Short Term Results for Novato Baylands ...... ES‐8 Figure ES‐3: Q50 ‐ Existing and Short Term Alternative Water Surface Elevation at MAX Flood ...... ES‐9 Figure ES‐4: Medium Term Alternative Elements ...... ES‐11 Figure ES‐5: Q50 Medium Term Results for Novato Creek ...... ES‐12 Figure ES‐6: Q50 ‐ Existing and Medium Term Alternative Water Surface Elevation at Max Flood .... ES‐13 Figure ES‐7: Long Term Alternative Elements ...... ES‐15 Figure ES‐8: Q50 Long Term Results for Novato Creek ...... ES‐16 Figure ES‐9: Q50 ‐ Existing and LONG Term Alternative Water Surface Elevation at Max Flood ...... ES‐17 Figure ES‐10: Q50 Peak Water Surface Profile – Diablo Ave. to (ft, NAVD88) ...... ES‐19 Figure ES‐11: Q50 Peak Flood Water Surface Elevations (Plan View) ...... ES‐21 Figure ES‐12: Q50 Peak Flood WSE Profiles – Existing Conditions and with 1‐ft and 3‐ft of Sea Level Rise ...... ES‐22 Figure 2 1: Novato Creek Watershed Topography and Drainages...... 2‐3 Figure 2 2: Novato Creek Channel Incision (left) and Bayland Deposition (right) ...... 2‐4 Figure 2 3: Boundaries of the integrated models ...... 2‐6 Figure 2 4: Boundaries and bathymetry (a. above) and model mesh (b. below) of the NHS Bayland Model ...... 2‐8 Figure 4 1: Short‐Term Alternative Elements ...... 4‐6 Figure 4 1a: Short Term Element 3, Restoration of Leveroni Creek Tributary Floodplain ...... 4‐7 Figure 4 1b: Short Term Elements 5‐6 ...... 4‐8 Figure 4 1c: Short Term Elements 7 through 9 ...... 4‐9 Figure 4 1d: Short Term Alternative Elements in the Baylands ...... 4‐10 Figure 4 2: Medium‐Term Alternative Elements ...... 4‐14 Figure 4 2a: Medium Term Alternative Upper Creek Elements: ...... 4‐15 Figure 4 2b: Medium Term Alternative Creek Elements Continued ...... 4‐16 Figure 4 2c: Medium Term Implementation Elements Upstream of Hwy 37 ...... 4‐17 Figure 4 2d: Medium Term Implementation Elements Downstream of Hwy 37 ...... 4‐18 Figure 4 3: Long‐Term Alternative Elements ...... 4‐21 Figure 4 3a: Long Term Implementation Elements Upstream and Near Hwy 37 ...... 4‐22 Figure 4 3b: Long Term Implementation Elements Downstream of Hwy 37 ...... 4‐23 Figure 5‐1: Q10 Existing Conditions Flood Depth (above) and Short Term Alternative Changes in Flood Plain Inundation (below) ...... 5‐9 Figure 5‐2: Q50 Existing Conditions Flood Depth (above) and Short Term Alternative Changes in Flood Plain Inundation (below) ...... 5‐10 Figure 5‐3: Q100 Existing Conditions Flood Depth (above) and Short Term Alternative Changes in Flood Plain Inundation (below) ...... 5‐11 i‐4

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐4: Novato Bayland Changes in Short Term Peak Flood Water Surface Elevations ...... 5‐12 Figure 5‐5: Q10+1ft ‐ Existing and Short Term Alternative Water Surface Elevation at Max Flood ...... 5‐13 Figure 5‐6: Q50 ‐ Existing and Short Term Alternative Water Surface Elevation at Max Flood ...... 5‐14 Figure 5‐7: Q100 ‐ Existing and Short Term Alternative Water Surface Elevation at Max Flood ...... 5‐15 Figure 5‐8: Novato Bayland Changes in Short Term Peak Flood Velocity ...... 5‐17 Figure 5‐9: Bed Shear Stress at Max Flood for Existing Conditions (above) and Short Term (Below) ... 5‐18 Figure 5‐10: Q10 Existing Conditions Flood Depth (above) and Medium Term Alternative Changes in Flood Plain Inundation (below) ...... 5‐22 Figure 5‐11: Q50 Existing Conditions Flood Depth (above) and Medium Term Alternative Changes in Flood Plain Inundation (below) ...... 5‐23 Figure 5‐12: Q100 Existing Conditions Flood Depth (above) and Medium Term Alternative Changes in Flood Plain Inundation (below) ...... 5‐24 Figure 5‐13: Novato Bayland Changes in Medium Term Peak Flood Water Surface Elevations ...... 5‐25 Figure 5‐14: Q10 – Existing and Medium Term Alternative Water Surface Elevation at Max Flood..... 5‐26 Figure 5‐15: Existing and Medium Term Alternative Water Surface Elevation at Max Flood ...... 5‐27 Figure 5‐16: Novato Bayland Changes in Medium Term Peak Flood Channel Velocities ...... 5‐28 Figure 5‐17: Bed Shear Stress at Max Flood for Existing Conditions (above) and Medium Term Alternative (below) ...... 5‐29 Figure 5‐18: Q10 Existing Conditions Flood Depth (above) and Long Term Alternative Changes in Flood Plain Inundation (below) ...... 5‐33 Figure 5‐19: Q50 Existing Conditions Flood Depth (above) and Long Term Alternative Changes in Flood Plain Inundation (below) ...... 5‐34 Figure 5‐20: Q100 Existing Conditions Flood Depth (above) and Long Term Alternative Changes in Flood Plain Inundation (below) ...... 5‐35 Figure 5‐21: Novato Bayland Changes in Medium Term Peak Flood Water Surface Elevations ...... 5‐36 Figure 5‐22: Q50 ‐ Existing and Long Term Alternative Water Surface Elevation at Max Flood ...... 5‐37 Figure 5‐23: Q100 ‐ Existing and Long Term Alternative Water Surface Elevation at Max Flood ...... 5‐38 Figure 5‐24: Novato Bayland Changes in Long Term Peak Flood Channel Velocities ...... 5‐40 Figure 5‐25: Bed shear Stress at Max Flood for Existing Conditions (above) and Long Term Alternatives (below) ...... 5‐41 Figure 5‐26: Valley Flood Inundation and Creek Depth Change at Q10: Existing/Short/Medium/Long (Clockwise Direction) ...... 5‐45 Figure 5‐27: Change in Valley Flood Inundation at Q10: Existing/Short/Medium/Long (Clockwise Direction) ...... 5‐46 Figure 5‐28: Novato Baylands Water Surface Profile at Q10 (above) and Q50 (below) at Max Flood for Existing/Short/Medium/Long...... 5‐47 Figure 5‐29: Q10 – Water Surface Elevation at Max Flood ...... 5‐48 Figure 5‐30: Existing WSE and Changes at Max Flood: Short/Medium ...... 5‐49 Figure 5‐31: Valley Flood Inundation and Creek Depth Change at Q50: Existing/Short/Medium/Long (Clockwise Direction) ...... 5‐50

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐32: Change in Valley Flood Inundation at Q50: Existing/Short/Medium/Long (Clockwise Direction) ...... 5‐51 Figure 5‐33: Water Surface Elevation at Max Flood Existing/Short/Medium/Long (Clockwise Direction) ...... 5‐52 Figure 5‐34: Existing WSE and Changes at Max Flood: Existing/Short/Medium/Long (Clockwise Direction) ...... 5‐53 Figure 5‐35: Longitudinal Profile of Flow Velocity at Max Flood ...... 5‐54 Figure 5‐36: Q50 – Existing WSE Changes with 1ft and 3ft Sea Leve Rise ...... 5‐56 Figure 5‐37: Time Series at Q50 of Existing and Short Term Alternatives WSE Times Series at Nave Gardens, Mid DIB and BMK North Lock: Existing Conditions, 1ft SLR and 3 ft SLR ...... 5‐57 Figure 5‐38: Q50 – Existing and Short Term Alternative WSE Profile at Max Flood with 1ft Sea Level Rise (above) and 3 ft Sea Level Rise (below) ...... 5‐58 Figure 5‐39: Q50 – Existing and Short/Medium/Long Alternatives Bayland WSEs at Max Flood with 3 ft Sea Level Rise ...... 5‐59 Figure 5‐40: Time Series at Q50 of Existing and Short Term Alternatives WSE Time Series at Nave Gardens, Mid DIB and BMK North Lock. Mid Tide Analysis ...... 5‐60

LIST OF TABLES Page No.

Table ES‐1: Novato Watershed Project: SHORT Term Alternative Summary ...... ES‐7 Table ES‐2: Novato Watershed Project: MEDIUM Term Alternative Summary...... ES‐10 Table ES‐3: Novato Watershed Project: LONG Term Alternative Summary ...... ES‐14 Table ES‐4: Changes in Effected Buildings with Alternative ...... ES‐19 Table 3 1: NHS Elements Summary (8 watershed/14 bayland) ...... 3‐3 Table 3 2: Novato Bayland Alternative Elements and Ranking Criteria ...... 3‐9 Table 3 3: Novato Creek Alternative Elements and Ranking Criteria ...... 3‐12 Table 3 4: Element Recommendations Not Modeled ...... 3‐14 Table 4 1: Novato Creek Elements in the Short Term Alternative ...... 4‐5 Table 4 2: Novato Creek Elements in the Medium Term Alternative ...... 4‐13 Table 4 3: Novato Creek Elements in the Long Term Alternative ...... 4‐20 Table 5‐1: NHS Alternative Analysis Results – Q10 ...... 5‐5 Table 5‐2: NHS Alternative Analysis Results – Q50 ...... 5‐6 Table 5‐3: NHS Alternative Analysis Results – Q50 ...... 5‐7 Table 5‐4: Predicted Peak WSEs for Novato Baylands ...... 5‐8 Table 5‐5: Predicted Peak Flood Velocities for Novato Baylands ...... 5‐16

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

1 EXECUTIVE SUMMARY The Watershed Program of the Marin County Department of Public Works (MCDPW) conducted this Novato Creek Hydraulic Study (the “NHS”) to identify and evaluate a suite of feasible alternatives to reduce Novato Creek flood hazards and on‐going sediment management effort and cost. Alternatives are to be designed in a manner that protects, if not enhances, sensitive habitat and species (particularly steelhead and Ca. Ridgway’s Rail) that reside in Novato creeks and baylands. This report presents the suite of recommended alternatives, and preliminary numerical modeling analyses used to evaluate the efficacy of recommended actions.

Kamman Hydrology & Engineering, Inc. (KHE) led the NHS study, with support from a consultant team which included WRECO Consultants (WRECO) and Dynamic Solutions International (DSI). WRECO and DSI conducted modeling analysis in the watershed and bayland respectively. MCDPW staff provided community and stakeholder outreach and coordination, and design storm and hydrology (rainfall/runoff) analysis. This NHS alternatives analysis is supported by prior NHS study phases,1 and by prior MCDPW flood and bayland studies and management actions. The focus of the

The Marin County Flood Control and Water Conservation District (District) and the Novato Flood Control Zone 1 Advisory Board have a long history of successful flood hazard mitigation work via the Novato Creek Flood Control Project (MCDPW, 1984). Multiple flood control projects have been implemented in the corridor to maximize flood conveyance and stabilize eroding banks in Novato Creek between Grant Ave. and Diablo Ave. The District dredges aggrading sediment between Diablo Ave. and the Sonoma Marin Area Regional Transit (SMART) Bridge every four years to maintain channel conveyance for the 50 year storm event. Routine channel maintenance also includes clearing trash and overgrown vegetation from the channel.

This study is a continuation of these efforts to further improve flood protection efficiencies and reduce the ecological impacts of flood and sediment management. The focus of the study is on flood protection improvements to the current Novato Flood Control Project which maintain 50 year flood protection. A secondary goal is to reduce sediment aggradation and the associated dredging costs, which improving habitat for special status in the area. Opportunities for improvement are greatest in Novato Baylands where MCDPW owns and manages both flood protection levees and most of the adjacent undeveloped bayland basin. This NHS study uses a watershed approach, and looks more broadly to identify opportunities for flood hazard mitigation both upstream and downstream of downtown Novato. While there is a good basis of information in prior flood control work in these downstream reaches. This is the first effort to characterize and evaluate

1 Prior site assessment phases characterized watershed conditions and configured/calibrated numerical models which predict Novato creek, bayland and overbank flows from Stafford Dam to San Pablo Bay (KHE, 2014).

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

opportunities for flood control improvement upstream of Grant Avenue (the limit of prior Flood Control study). The NHS study has the following objectives:

 Evaluates the impacts and recommends mitigation measures to maintain or improve the flood conveyance capacity now and in the future assuming that sea level rise and increasing storm intensity will increase watershed flood hazards;  Integrates consideration of riparian corridor as habitat for fish and wildlife, and identifies actions which concurrently support the ecological values of the watershed.  Considers geomorphic processes (sediment transport, deposition and scour) in the design and evaluation of flood mitigation in an effort to reduce channel maintenance costs and impacts;  Defines and evaluates measures to reduce the impacts associated with overbank flooding;  Evaluates tidal influences on low lying reaches of Novato and Warner creeks below Seventh St./Tamalpais Ave.; and,  Evaluates actions in the tidal baylands to reduce dredge maintenance by expanding the creek corridor and restoring subsided tidal wetland to store aggrading sediment.

Current conditions in Novato’s creek corridors reflect changes due to urbanization. The prior existing conditions assessment (KHE, 2014) and monitoring found that despite successful efforts to maximize conveyance, both Novato Creek and Warner creek currently flow at or near bankfull in a 10‐20 year event. Warner Creek (from McClay Ave. downstream) and Novato Creek (Grant Ave.to Diablo Ave.) are the focus of ongoing work to provide 50 year flood conveyance with minimal out of channel flooding that doesn’t inundate residential and commercial living space. There are several reasons why Lower Novato Creek may not contain a 50 year design flow including: 1) updated MCDPW/WRECO generated design storm estimates reflect the more recent, larger magnitude storm events; and 2) the more detailed hydraulic modeling in the watershed characterizes both instream and overbank flows more accurately, providing a better accounting of the water that flows out of bank but returns to the same drainage. Because flooding is anticipated during large storm events, the NHS study sought to identify and evaluate measures which reduce the adverse impacts of overbank flooding.

The NHS uses a consensus based approach supported by public and private stakeholders to identify and select study alternatives. MCDPW defined a list of recommended project “elements2” based on watershed existing conditions, and opportunities/constraints assessments. After identifying the

2 An “element’ is a group of actions which satisfy identified NHS study goal (e.g. reduce flooding in known location).

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

elements, the team worked with project stakeholders3 to define ranking criteria which considered flood control, implementation feasibility, ecological impact/benefit and cost. Stakeholder and public meetings were held to develop consensus on the elements, evaluation criteria and ranking. KHE then used these criteria to evaluate, rank and group elements to create three (3) recommended alternatives that reflect stakeholder’s priorities, and the technical study team’s understanding of current watershed and bayland flood hydraulics4.

Alternatives are evaluated via numerical models which permit comparison of Existing and Alternative flood impacts. The study focuses on flood conditions associated with a 10‐year (yr.), 50 yr. and 100 yr. storms, and the effects of 12” and 36” of sea level rise (SLR) in San Pablo Bay. Evaluation of creek and bayland actions together is necessary for the NHS study because the City of Novato is susceptible to flooding from watershed runoff (upstream), which is made worse by high tides (downstream) that reduce City drainage capacity. As a result, actions are required to address flooding in Novato from both upstream and downstream sources. To facilitate planning and implementation, the alternatives are organized into those elements recommended for implementation in SHORT (5‐10 years), MEDIUM (10‐15 yr.) and LONG (20+ yr.) term action plans.

1.1 Summary of Study Alternatives: The overarching goal of the study is to reduce peak flood water surface elevations, and increase flood and sediment conveyance, while improving ecological conditions in the corridor. Creek elements decrease flooding by adding Stafford Dam, floodplain and detention storage, and by improving drainage in areas where flooding occurs. Baylands elements expand the currently leveed floodplain using storm water spillways or breaching (via levee removal) to tidal basins adjacent to Novato Creek. Each of the recommended study alternatives (Short, Medium and Long) creates an incremental decrease in peak flood water surface elevation or increases conveyance capacity as compared to existing conditions5. Actions selected for future consideration were grouped based primarily on implementation constraints.

 Short Term Actions: Actions that can be constructed in 5‐10 year planning and implementation horizon. Multiple Bayland actions can be implemented in the short term. The most significant short term benefits can be realized in the Upper Baylands and adjoining low lands at or below 14 ft.

3 Primary stakeholders in the NHS study included the City of Novato, North Marin Water District, Novato Sanitary District, the Bel Marin Keys Community Services District, the Ca. Coastal Conservancy, and interested public members. 4 Watershed conditions were characterized via flow monitoring, watershed and geomorphic field assessment, and calibrated numerical models developed for the project in Phase II. 5 The NHS utilized numerical models to evaluate and characterize the hydraulic benefit of each Alternative.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

 Medium Term Actions: Actions that can be constructed in a 10‐15 year planning and implementation horizon. Actions that require additional studies, landowner coordination and possibly acquisition or easements to implement. Addition of flood storage at Stafford Dam and on the upper Novato Creek floodplain yield significant flood reductions for City parcels. Lower Bayland levee realignments downstream of Highway 37 expand flood mitigation benefits downstream.

 Long Term Actions: Actions that can be constructed in a 20+ year planning and implementation horizon to support long term adaption to increasing storm magnitudes and sea level rise. Actions modify City storm drain and street infrastructure to increase City flood conveyance and storm water drainage along designated urban drainage corridors (floodways). Bayland coastal flood protection is shifted landward to upland boundaries to the extent feasible.

Short Term Alternative: The Short Term Alternative consists of those actions that can be constructed in 5‐10 year planning and implementation horizon. Figures ES‐1 shows the location of the Short Term Alternative elements. A brief description of the elements and their estimated costs are presented in Table ES‐ 16. Short term actions will required additional funding, study, modeling, design and environmental compliance before they can be constructed.

In this preliminary look at flood control options upstream Grant Ave, several Short Term actions considered upstream of Simmons Lane were eliminated because, although they increased flood conveyance as intended, they also increased flooding downstream. This occurs because Novato creeks flow at or above capacity during large storm events, so actions which reduce overbank flooding upstream convey more water downstream. Given the constraints posed by the limited available downstream capacity in the Novato Creek, Warner Creek and Rush Creek drainages, no Short Term measures were identified to mitigate for the impacts of added upstream inflows. As a result, at Q50, the short term alternatives have limited benefits upstream of Diablo Ave. (Figure ES‐ 2). In this and all alternatives, flood reduction benefits are greater at lower flows, as illustrated by analysis of the 10‐yr. storm event. However, more opportunity for flood mitigation exists in the undeveloped baylands. The Short Term Alternative makes use of MCDPW’s expansive diked bayland parcels to attenuate flood peaks one to three feet, and accelerate flood recession in the corridor (Figure ES‐3). The result is a significant decrease in peak flood water surface elevations (1‐3 ft), and an increase in sediment conveyance capacity through the dredge reach which can be expected to reduce the frequency of maintenance dredging. The increase in tidal prism in the upper bayland provides downstream benefit in a corresponding increase in the self‐sustaining channel

6 Attachment B provides a detailed description of elements.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

geometry (width and depth) in the lower bayland. This is expected to reduce the frequency and extent of maintenance dredging required downstream of Hwy37.

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Figure ES‐1: Short Term Alternative Elements

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Table ES‐1: Novato Watershed Project: SHORT Term Alternative Summary

Note: Costs presented here and throughout the document are based on conceptual designs. Estimates reflect 2016 Bay Area construction costs (RSMeans, 2015) and costs for similar projects constructed in the bay area in the past 1‐5 years. Costs are intended to support planning, and for comparison between element actions, and do not include escalations for inflation, overhead and profit.

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EXISTING

SHORT

Difference (SHORT minus EXISTING)

Figure ES‐2: Q50 Short Term Results for Novato Baylands ES‐8 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

EXISTING

SHORT

Difference (SHORT minus EXISTING)

Figure ES‐3: Q50 ‐ Existing and Short Term Alternative Water Surface Elevation at MAX Flood ES‐9 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Medium Term Alternative: Medium Term elements are those that can be implemented in a 10‐15 year time frame. Figure ES‐4 maps the elements which make up the Medium Term Alternative. A brief description of the elements and their estimated costs are presented in Tables ES‐2. The greatest reduction in depth and extent of City flooding occur as a result of the concurrent increase of flood storage and floodplain attenuation upstream of Sutro Ave. In the tidal baylands, expanding the corridor at Hwy 37 and breaching the eastern portion of the lower Bayland further reduces flood peaks throughout the baylands, and accelerates flood recession in lower Novato Creek. Flooding around Pacheco Pond is limited via design of alternative discharge points to the BMK Restoration site. Medium term actions reduce the percentage of building flooded within the study area by 5%, and lower peak WSE 1‐3 ft. throughout the Bayland corridor, effectively constrain flooding (Figures ES‐5 and ES‐6). Table ES‐2: Novato Watershed Project: MEDIUM Term Alternative Summary

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Figure ES‐4: Medium Term Alternative Elements

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Figure ES‐5: Q50 Medium Term Results for Novato Creek

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EXISTING

MEDIUM

Difference (MEDIUM minus EXISTING)

Figure ES‐6: Q50 ‐ Existing and Medium Term Alternative Water Surface Elevation at Max Flood ES‐13 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Long Term Alternative: Long Term elements are those that can be implemented in a 20+ year time frame. Implementation of these actions support long term adaption to increasing storm magnitudes and sea level rise and including infrastructure relocation or modification. Figures ES‐7 maps the elements which make the Long Term Alternative. A brief description of the elements and their estimated costs are presented in Tables ES‐3. Long term actions in the Novato’s creek corridors expand medium term work in upper watershed floodplain restoration and in lower watershed storm drain and surface street improvements. City flooding is reduced primarily by engineering overland conveyance corridors to restrict floodplain inundation, and increase storm water drainage efficiency (Figure ES‐8). Long term actions in the Bayland relocate much of the remaining flood control infrastructure to the upland perimeter, while maintaining coastal flood protection for Hwy 37 and the recently improved railroad ROW (Figure ES‐9).

Table ES‐3: Novato Watershed Project: LONG Term Alternative Summary

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Figure ES‐7: Long Term Alternative Elements

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Figure ES‐8: Q50 Long Term Results for Novato Creek

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EXISTING

LONG

Difference (LONG minus EXISTING)

Figure ES‐9: Q50 ‐ Existing and LONG Term Alternative Water Surface Elevation at Max Flood ES‐17 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

1.2 Alternatives Analysis The NHS study utilizes numerical models to evaluate the efficacy of study alternatives based on the change in conditions from those predicted for existing conditions in the watershed. Changes in the extent of flooding are depicted on plan maps, and quantified based on the number of building impacted. In the largely undeveloped bayland, the analysis looks at the change in flood WSE maxima and changes in flooded area. Bayland analysis also evaluates the change in the water surface gradients during flooding and flood recession. These gradients drive the transport of water and sediment into and across the bayland. Flow velocity and shear stress profiles/maps were also evaluated as a measure of resulting change in sediment transport capacity or flood recession rate across the bayland.

In the Novato/Warner Creek drainages maximum flood WSEs are reduced along the creek corridors (due to upstream changes), and in low lying areas which accumulate overbank flows from upstream and/or benefit from WSE reductions created by bayland actions. The greatest benefits are observed at Q107 flows, with lesser benefit found at Q50/Q1008. Per Table ES‐4, at Q10, short term actions yielded a 13% reduction in building impacted, while medium and long term alternatives yielded a 40% reduction. At Q50 short term actions yield nominal benefits (flood impacts were reduced less than 1% across the valley floor) while medium and long term actions yield only a 6‐8% reduction in buildings impacted for Q50 and Q100 flows respectively. Benefits for Q50 flows occurred primarily in Nave Gardens and downstream where both a pump and bayland reductions occur. Within these areas are critical City of Novato fire and hospital facilities. All Alternatives yielded small benefit at higher flows because they only partially alleviated flooding at Q10, and could provide minimal additional benefit for the added Q50/100 volumes. Given the limited peak flood water level reduction predicted upstream of Diablo Avenue, Chapter 6 recommends additional study and evaluation of modified and additional elements.

7 Q10, Q50 and Q100 refer to design storms of increasing magnitude. The number references the probability of occurrence of a storm event of a given size in any given year. For example, a Q10 event, commonly referred to as a 10‐ year storm, has a one in ten probability or 10% chance of occurring in any given year. The 50‐year (Q50) and 100‐year (Q100) storms have a 2% and 1% probability of occurrence in any given year. 8 In general, Q50 and Q100 storms have a comparable peak flood WSE. Q100 storms have a greater duration and storm volume.

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Table ES‐4: Changes in Effected Buildings with Alternative Alternative Buildings Effected Reduction in % Reduction of by 6” or Greater Number of Effected Flood Depth Building Effected Buildings Existing Conditions(Q10) 419 Short Term (Q10) 365 54 13% Medium Term (Q10) 251 168 40% Long Term(Q10) 253 166 40%

Existing Conditions(Q50) 1214 Short Term (Q50) 1202 12 1% Medium Term (Q50) 1154 60 5% Long Term(Q50) 1112 102 8%

Fortunately, in stark contrast to the urbanized creek corridor, the large amount of capacity available in the Novato Baylands provides significantly more opportunity for flood mitigation. East of Hwy 101, maximum flood WSEs decrease with distance downstream under both existing and proposed conditions. When compared to current conditions, all alternatives reduce peak flood water surface elevations across the baylands, reduce the areal extent of flooding and increase bayward flow and sediment transport gradients from tidally influenced reaches as far upstream as Diablo Avenue.

Figure ES‐10: Q50 Peak Water Surface Profile – Diablo Ave. to San Pablo Bay (ft, NAVD88)

Figure ES‐10 presents the predicted Q50 peak flood WSE profiles from Diablo Ave, to San Pablo Bay. Short (red), Medium (blue) and Long (green) Term Alternatives reduce peak flood WSEs by 1‐3 ft., with benefits attenuating with upstream and down from actions. Increases in Lower Novato and

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Warner Creek drainage are supported by all bayland actions, which reduce peak flood WSEs at Diablo Ave. by approximately 0.5‐1 ft. at all evaluated discharges9. Within the baylands, all Alternatives create a stepped flood profile which reflects increased flow and sediment movement into restored basins, and a reduction in conveyance in the basins where flood waters slow across the expanded floodplain and sediment is deposited. Predicted velocities within the Novato baylands becomes less uniform with each alternative. Novato Creek channel velocities increase through the dredge reach and where the channel narrows. Concurrently, channel velocities rapidly decrease where flows enter newly created tidal basins. This hydraulic structure results in an increase in sediment conveyance toward the newly restored tidal basins, and sediment deposition within the basins. The rate and location of sedimentation will depend on frequency, magnitude and recurrence of storm events.

In Novato Baylands flooding begins in the corridor near Hwy 37, with upstream and then downstream areas flooding shortly thereafter. Figure ES‐11 maps Q50 WSE peaks and the areal extent of flooding for existing conditions and study alternatives. Along the Novato Creek corridor, color shifts from warm to cool indicate decreasing flood stage. Basins newly open and flooding are depicted. Basin WSE maxima are not shown because flooding continues to expand across the bayland following flood peaks, and subsequent high tide periods. Of equal importance is the increase in the slope (color shift) within the Novato Creek channel between the creek confluence and the bayland, which indicates the strength of the bayward gradients in peak flood. In all design storms, the Alternatives increase this slope. In addition to attenuating peak flood WSE, expansion of the bayland tidal floodplain also reduces the tidal amplitude in non‐flood conditions. This enhances the flood mitigation benefits by lowering the starting water surface elevation in basins, and increasing potential storage capacity in the tidal basins.

Short term actions lower flood stages both in the upper bayland and in the dredged confluence reach upstream. Restoring tidal wetlands at West Basin does not provide a comparable amount of flood relief upstream because the channel cross section is at a minimum at Hwy 37, and limits conveyance in in adjacent bayland reaches. Flooding is reduced on the adjacent BMK and private agricultural lands downstream. With the expansions of the Hwy 37 crossing and restoration of tidal wetlands in Deer Island and East Basins, Medium term elements create larger and more wide spread reductions in flood WSEs, and eliminate Q50 flooding along the Novato Creek corridor, at Hwy 37 and at BMK. Long term actions further expand wetland restoration and reduce Q50 and Q100 peak flood WSE to below the current FEMA base flood elevation (BFE) of 10 ft. NAVD88.

9 Diablo Ave. is the approximately the limit of both current tidal influence and bayland actions benefit in the corridor.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure ES‐11: Q50 Peak Flood Water Surface Elevations (Plan View) ES‐21 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure ES‐12: Q50 Peak Flood WSE Profiles – Existing Conditions and with 1‐ft and 3‐ft of Sea Level Rise

1.3 General Flood Study Findings: Presented below are general findings for the Novato Creek Hydraulic Study. These findings present both the improved understanding of watershed conditions, and the analysis of study alternatives.

1. The 1984 Novato Flood Control Project maximized conveyance through the Novato Creek study area. Despite these actions, Novato and Warner Creeks are both near conveyance capacity at Q10 or greater discharges. . Ongoing floodplain development has further impacted (reduced) flood storage and infiltration on the valley floor increasing runoff to Novato’s creeks . Existing bridges pass flood waters and are not point sources of flooding . Channel area decreases downstream as discharge accumulates and generates overbank flooding . Novato and Warner Creeks conveyance downstream of Seventh St. is reduced during high tide events.

ES‐22 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

2. In Q10 storm events:  Flooding occurs on Novato and Warner Creeks within the City limits and in the Novato Baylands  Novato Creek overtops its banks and produces flooding upstream of Simmons Lane and downstream of Seventh St. where accumulating inflows exceed channel capacity. Flooding along Novato Creek extends north toward Railroad Ave. which discharges to Rush Creek, and South toward Warner Creek. Flooding at both these locations results from both local high water in the creeks and the accumulation of floodwater from upstream watershed areas. . The valley floor dips south, conveying much of Novato Creek overbank flows upstream of Grant Ave. toward Warner Creek. . Warner Creek floods parcels north of the creek downstream of Seventh St., and south of the creek downstream of Diablo Ave., along both Center Rd. downstream of McClay Rd. and South Novato Blvd. . Novato baylands flooding starts at the narrowed Hwy 37 crossing and subsequently tops north and south levees at Pacheco Pond.

3. In larger storm events:  Flooding is concurrent on Novato and Warner Creeks, and there are no alternate routes with capacity  Flooding along the narrows between Miwok and Pioneer Parks acts to reduce flood pressure downstream on Novato Creek  This overbank water flows west/south from Novato Cr. to Warner Cr. and beyond, and increases flooding in Warner Creek drainages  City storm drains exceed capacity and/or backwater creating localized flooding: upstream of Miwok Park; in the Rush Creek corridor: and in the lower Warner Creek drainage downstream of Seventh St along Center Rd. and So. Novato Blvd (Nave Gardens)

4. In a Q50 storm event: Creek flooding extends over much of the valley floor along both Warner and Novato Creeks. Flood depths are typically less than one foot. Flooded depths of 1‐3 feet occur:  Adjacent to Vineyard Creek between Wilson Ave. and McClay Rd.;  Along Warner Creek from Grant Ave. to So. Novato Blvd;  Along Novato Blvd. upstream of Grant Ave.  Southeast of Diablo Ave. where high tides restrict drainage and accumulated water spreads north along Railroad Ave. and south along So.o Novat Blvd. /Center Rd. . Downstream of Seventh St, Novato Creek flooding and backwater from adjacent storm drains collects to the north along Redwood Blvd., and then flows north toward Rush Creek. Storm drain and creek outfalls along the Rush Creek drainage also do not have

ES‐23 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

adequate storm capacity, and discharges to the north result in Rush Creek drainage flooding. . Bayland flooding expands along the Hwy 37 corridor and at Pacheco Pond, inundating adjacent parcels. In addition, levees are overtopped adjacent Hwy 101, along the BMK Community North Lagoon, and at Lynwood and North Deer Island Basins. . High water levels are sustained in throughout Novato Creek for more than 4 days following the 48‐hr. storm event, reducing drainage capacity from storm drains and outfalls.

5. In a Q100 storm event:  Peak flood discharges are comparable to Q50 flood maxima, because Novato’s creeks overtop their banks at the same elevations. The Q100 storm duration and volume are greater than the Q50 storm, and results in deeper and more contiguous flooded areas encompassing much of Novato between Center Rd. and Grant Ave.  The greatest increase in creek flooding occurs along the Warner Creek corridor which receives both upstream tributary inflows and overbank Novato Creek water. When Novato Creek overtops its banks, flood waters flow south across Novato Blvd. and into the Warner Creek drainage both upstream of McClay Rd. and downstream of Seventh St /Tamalpais Ave.  Bayland flooding expands cutting off access to critical facilities, inundating NSD treatment facilities, obstructing Hwy 37, and inundating buildings around Pacheco Pond and at BMK. 6. Peak Flood Water Surface Elevations (WSEs):  Are comparable for Q50 and Q100 storm events because overbank flooding limits the maximum creek stage.  Rise at comparable rates in both Novato and Warner creeks  Decrease with distance downstream from Stafford Dam to San Pablo Bay  Decrease rapidly within the confluence reach where the valley floor transitions to bayland creating a strongly depositional environment.  Increase locally and create flooding at the Hwy 37/Railroad crossing due to narrowed levee alignments and an aggraded channel  Decrease rapidly with floodplain expansion and support natural deposition in Novato’s subsided bayland basins

7. Sea Level Rise  Can be expected to increase bayland water surface elevations 1‐3 feet within the 50‐year design horizon of the NHS study.  Will increase daily tide maxima to 8‐10 ft.

ES‐24 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

o Downstream of Hwy 37, this increases both daily tide range and peak flood water surface elevation (WSEs). The daily tidal maxima will increase to near or above current Q50 flood maxima, and results in less than 2‐3 ft of levee freeboard on most bayland levees o Upstream of the Hwy 37 this increases does NOT increase peak flood WSEs because flood stages rise above tidal influence to 10‐16 ft.  Reduces City outflow capacity and increases sedimentation in the already aggrading Novato/Warner Cr. confluence reach between Diablo Ave. and Rowland Ave.  Decreases bayland velocity maxima and slows flood recession in Novato/Warner Cr and across the baylands  Is expected to continue, reaching 4.5 ft. by 2100 (BCDC, 2014), propagating impacts upstream, and requiring increasing dependence on storm water storage during high tides.

8. Levee Setbacks (Relocation of Bayland Levees to widen the creek corridors):  Reduce peak sflood WSE by expanding the available conveyance area. These reductions will diminish over time due to sea level rise  Increase the rate of flood attenuation and recession  Increase bayward flow and sediment transport capacity during favorable tides  Increase tidal prism (the volume of water exchanged daily by the tide) and in turn the size of the channel that is maintained without dredging during low flow conditions.  Provide capacity for natural sedimentation and passive climate adaption via landscape response  Improve the extent and ecological values of tidal wetlands and the Novato/Warner Creek corridors

9. Tributary Floodplain Restoration: Benefits are limited in the extreme design storm events because elements do not retain a sufficient volume to provide downstream benefit  At lower flow regimes, elements attenuate flooding, support ground water recharge in the riparian corridor ecotone, and reduces sediment loading to the creek  Would require addition of main stem floodplain elements to increase floodplain storage, reduce downstream flow velocities and bed/bank erosion during large storm events.

10. Drainage Improvements in Lower Warner Creek Basin  Increase the storm drainage volume by 30‐50%, with adequate downstream storage.  Significantly increase flood conveyance capacity and are not limited at high tide  Do not decrease peak flood WSEs locally because of the added upstream inflows  Increase the rate of overbank flood recession following large storm events

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 Warrant further consideration despite the limited reduction in peak flood water surface maxima

1.4 Alternative Analysis Conclusions Short, Medium and Long Term Alternatives provide an incremental reduction on overbank flooding with each Alternative. Conclusion and recommendations for each alternative are presented below. This preliminary study evaluates Alternatives, groupings of elements, but does not quantify the benefits of individual elements. In general, Bayland actions yielded a larger reduction in peak flood WSE than creek actions. Additional dam storage and upper creek floodplain restoration appear to have the most significant benefits in non‐tidal reaches. In the Baylands, levee setbacks and tidal wetland restoration yield significant benefit, which increases with the scale of action. Upper bayland actions yield benefits which impact both upstream reaches and down, and as such, have the greatest efficacy.

Short Term Elements: The most effective short term elements are the ensemble actions in the upper baylands which expanded the available conveyance corridor (Element 3) and add tidal prism and sediment storage capacity (Element 7B). Implementation of the Short Term Alternative: . Incrementally decrease but do not eliminate creek and bayland flooding . Have the greatest benefit in Novato Creeks at Q10, and limited benefit at Q50 and Q100 when the creek flows significantly exceed capacity10. . Increase flood recession rates and accelerate drainage from low lying areas . Increase flood conveyance capacity on Warner Creek during high tides by routing water downstream via Scottsdale Marsh and Lynwood Basin . Reduce bayland WSE maxima (1‐3+ ft.) and the location and volume of flooding . Limit Q10 bayland flooding to areas around Hwy 37 . Increase dredging efficiency without increased flooding . Add valuable estuarine habit . Yield benefits upstream of Hwy 37 due to added conveyance capacity in the creek corridor, which increases gradients from the dredge reach to the upper bayland, and adds storage capacity to potentially reduce the dredging frequency for aggrading sediment. . Yield benefits downstream of Hwy 37 in that the Short Term alternative increases tidal prism upstream of Pacheco Pond by over 500 ac‐ft., reducing the need for dredging in both the confluence reach, and in the Lower Baylands. Based on hydraulic geometry this is expected

10 Peak flows recorded at the USGS Gauge at Novato Creek (Gauge 11459000) during the available period of record (1947 – 2015) exceed the 10‐year recurrence interval a total of 6 times; the 5‐year recurrence interval 2 times and; the 100‐year recurrence interval 1 time. Recurrence estimates are from reported values provided in the FEMA FIS report 2014.

ES‐26 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

to yield an equilibrium channel width of > 200 feet (more than two times the existing channel width), and a 2‐3 foot decrease in channel depth. . Support sea level rise adaption by reducing daily tide range

Medium Term Elements: The most effective medium term elements are the increase in Stafford Dam storage (Element M‐ 1), excavation to increase conveyance at Hwy 37 (Element M‐6), restoration of tidal exchange in half of No. Deer Island Basin (Element M‐9) and East Basin (Element M‐11). Implementation of the Medium Term Alternative:  Significantly, reduces flooding across the watershed when compared to short term elements  Adding dam storage (700 ac‐ft) and floodplain restoration in upstream reaches of Novato Creek provides the most significant reduction in the downstream flood volumes, allowing Novato Creeks to contain and convey a larger percentage of overbank waters.  Incrementally reduce bayland peak flood WSEs by attenuating peak flood volumes and lowering the daily tide range, and in turn, pre‐storm starting water levels across the bayland  Increase drainage capacity and sediment conveyance rates from low lying creek and watershed areas  In Novato baylands, contain and convey the 50 year storm events without overbank flooding  Excavation of channel and marshplain at Hwy 37 removes a critical conveyance constriction at Hwy 37, increasing flow and sediment conveyance throughout the baylands  Incorporate expansive East Basin levee and infrastructure setbacks in the lower Novato baylands which lower flood peaks downstream of Hwy 37, increasing conveyance throughout the bayland and downstream by expanding channel geometry at the Novato Creek/San Pablo Bay confluence.

Long Term Elements: The most effective long term elements are the expansion of tidal exchange in No. Deer Island Basin (Element L‐3), and the restoration of O’Hair Park Floodplain (Element L‐1). Implementation of the Long Term Alternative:  Expand the work of medium term actions  Improve flood conveyance and reduce flooding in both the Creek and Bayland corridors  Work to reduce the impacts (extent and duration) of flooding in City streets by expanding undersized storm drains and establishing corridors which constrain and convey overbank flows  Reduce peak flood WSE an addition 2 ft across the baylands  Remove upland fill in bayland levees for beneficial reuse within the watershed  Reduce the opportunity for future expansion of storm water storage capacity in North Deer Island basin (Additional consideration of the future needs for storm water storage is warranted prior to conversion of all of Deer Island Basin to tidal wetland.)

ES‐27 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

1.5 Sea Level Rise Impacts Seal level rise analysis provided the most positive findings for the non‐tidal reaches of Novato creeks (Figure ES‐12). One to three feet of sea level rise did not impact peak flood water surface elevations in Novato/Warner Creeks upstream of Hwy 37. However, rising tides reduce creek flood recession rates and bayward sediment transport gradients during both typical and large storm events. SLR will increase sedimentation rates in the dredge reach and around low lying channels and outfalls, increasing the need mitigating bayland actions, and necessitating raising or increased maintenance for low lying outfalls.

Upstream of Hwy 37, in the 10‐15 year design horizon, Short Term bayland actions provide mitigating measures for more than 1 foot of sea level rise. However, analysis of 3 foot SLR scenarios indicate that as sea level continues to rise, these improvements are not sufficient to mitigate the impacts of progressively rising tides. Downstream of Hwy 37, sea level rise increase peak flood WSEs, and with 3 ft SLR has an added adverse impact in that daily high tides rise to 9‐10 ft. As normal tidal creek stages rise to within 2 ft of typical levee grades, the available freeboard for storm outflows decrease and overtopping risks rise. This rise in daily tide and storm peaks indicates that infrastructure improvements will be required to maintain existing levels of coastal flood protection. As a result, managed retreat is advisable to reduce long term maintenance costs for undeveloped basins east of Hwy 37.

1.6 Recommendations Priorities for Next Phases of Work  Upper bayland short term elements which maximize downstream flow and sediment conveyance and increase downstream sediment storage capacity  Lower Warner drainage improvements to increase conveyance from So. Novato/Center Rd via Scottsdale Pond. Efforts should first meet capacity needs for Lower Warner Creek drainage before increasing Arroyo Avichi diversions.  Beneficial reuse of dredged creek sediments and levee fill. This coarse sediment is a valuable resource and should retained and utilized for anticipated levee improvements and/or realignment  Further evaluation of Medium Term elements which provided significant benefits and thereby may warrant reconsideration as short term actions: o Raise Stafford Dam and/or add storage upstream to reduce flood volumes o Expansion of Novato Creek at Hwy 37 to improve overall bayland flood and sediment conveyance

Additional Projects: The following additional projects should be considered as part of short term work and funding requests

ES‐28 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

 Pacheco Pond water quality improvements – potential actions include o Improving circulation by modifying connector channel and/or inlet culverts o Increasing DO via aeration or reduction of nutrient loading o Excavation of organic rich sediment and decaying plant debris  Coarse sediment management along Novato and Warner Creeks. Actions could include: o sediment removal from accessible aggrading bars o grade control structures to limit Warner Creek incision o Arroyo Avichi sediment removal upstream of the diversion to reduce confluence reach sedimentation locally and upstream o localized riparian floodplain restoration to reduce vegetation encroachment support channel storage  City Storm Drainage Improvements to address capacity issues at: o Diablo Avenue discharging to Warner Creek o Grant Avenue outfall to Novato Creek o Sunset Parkway storm drains discharging to Lynwood Slough o North Railroad Ditch at Olive Avenue o San Marin/Mount Burdell inlets discharging to Novato Creek (sediment management)

Additional Study: The follow concepts warrant additional study to reduce flood risks and impacts, improve sediment management and ecological conditions in the watershed:

 Evaluate Novato Creek main stem floodplain restoration, prioritizing work at and upstream of the Bowman Cr. confluence to: o Increase flood storage and reduce peak flood flows o Reduce peak flow velocities and downstream scour and sediment transport o Increase ground water recharge and ecological conditions in the riparian corridor

 Integrate Upper Creek floodplain restoration actions with raising Stafford Dam to mitigate Dam impacts, and maximize flood storage and peak flood attenuation upstream of Novato’s urban center

 Evaluate surface street/storm drain/sanitary line improvements along “floodways” to o reduce the impacts of extreme floods on property and infrastructure o increase flood recession rates and lessen the duration of storm impact o maintain access to critical facilities during storm events

ES‐29 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

 Evaluate additional options to increase flood storage and/or flow diversion upstream of Simmons La. Including: o Storage above Stafford Dam o Novato Creek floodplain enhancements upstream of Sutro Ave o Diversion of San Marin area drainages to Rush Creek Marsh o Local detention storage for tributary drainage areas

 Evaluate feasibility and costs benefit of realignment of lower bayland levees parallel to Hwy 37, to reduce the total length of levee required. Levee realignment and basin restoration would entail the loss of most of NSD summer irrigation disposal capacity, would result in a realignment of Novato Creek in the lower bayland, and could adversely impact navigable access from the BMKCSD to Novato Creek.

ES‐30 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

2 INTRODUCTION The Novato Flood Protection and Watershed Program is one of several initiatives under the Marin County Watershed Program, which was approved by the Marin County Board of Supervisors in May 2008. The goal of the Watershed Program is to develop a framework that integrates flood protection, creek and wetland restoration, and fish passage and water quality improvements with public and private partners to protect and enhance Marin’s watersheds.

The Novato Watershed Program sought a system‐wide analysis of flood protection options to identify and evaluate a suite of feasible alternatives to integrate flood protection goals and sediment management efforts with creek and wetland restoration elements and habitat enhancement that protects sensitive species (particularly steelhead and Ridgway’s rail) that reside in Novato creeks and baylands.

This process began with a detailed description of the current status of creek, baylands, flooding, and habitat conditions as detailed in the Hydraulic Assessment of Existing Conditions (KHE, 2014). The existing conditions analysis was followed by modeling and analysis of potential alternatives that would reduce flood protection maintenance costs and impacts, restore habitat, and be resilient to sea level rise.

Project Goals: The overall Hydraulic Study goals are to identify and evaluate a suite of alternatives to: 1. Maintain and improve the existing level of flood protection, with a goal of achieving 50‐yr flood protection; 2. Reduce dredging costs and associated impacts by reducing the frequency and/or the extent of current dredging; 3. Improve the efficiency of flood control operations and maintenance, including sediment management; 4. Utilize and support natural processes to improve management efficiency and protect and enhance habitat for species of interest, particularly steelhead and Ca Ridgeway Rail; 5. Support integrated and multi‐benefit project alternatives ; and, 6. Adapt to climate change.

This report documents the alternatives selection process, describes the suite of recommended alternatives, and presents the numerical modeling analyses used to evaluate the efficacy of recommended alternatives. Prior watershed assessment and existing conditions (KHE, 2014) serves as the basis for the identification and evaluation of alternatives; and 5) utilize and support natural processes to improve bayland sediment management efficiency, and adapt to climate change.

2‐1 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

The Hydraulic Study Team: The Hydraulic Study team and concept development was led by Kamman Hydrology & Engineering, Inc. (KHE), WRECO Consultants (WRECO) and Dynamic Solutions International (DSI) assisted in the application of numerical hydraulic models which route rainfall from headwaters below Stafford Dam to San Pablo Bay. These models are used to evaluate the efficacy of proposed alternatives to improve flood and sediment management and natural resource values in the watershed. DPW staff complete the team, providing current systems operations information, engineering hydrology, and coordinating and facilitating meetings between the Hydraulic Study team, stakeholders and the public.

Project Partners: Marin County, City of Novato, Novato Sanitary District, North Marin Water District. Key stakeholders include Bel Marin Keys Community Service District, Marin Audubon Society, Ca. State Coastal Conservancy and many other who participated through technical working groups.

This report describes alternative development and modeling analysis undertaken to define and evaluate actions which meet these project goals. The County, the City of Novato, and the Novato Flood Control Zone No. 1 Advisory Board have a long history of successful flood hazard mitigation work, including implementation of the Novato Creek Flood Control Project (MCDPW, 1984). This work took place from 1985‐2006 and focused on maximizing flood conveyance and stabilization of eroding banks in Novato Creek between Grant Ave. and Diablo Ave. This study is a continuation of those efforts to further improve the level of flood protection and begin adaptation to climate change and sea level rise.

2‐2 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

2.1 Physical Setting The Novato Creek watershed is the largest watershed in eastern Marin County, encompassing a 44 square mile drainage extending eastward from relatively steep, predominantly undeveloped, convex hill slopes, across a suburban valley bottom in the City of Novato, and across an expansive leveed intertidal Bayland (Novato Baylands) to San Pablo Bay (Figure 2‐1). The watershed is approximately 17 miles long with elevations ranging from approximately 1900 ft. (NAVD88) at ridge top to sea level at the terminus with San Pablo Bay. It is bordered by coastal hills to the west, the basin and San Pablo Bay to the northeast and east, and the Miller Creek watershed to the southeast. Stafford Lake, with a storage capacity 4,450 acre ft, is a water supply reservoir operated by North Marin Water District, and it separates the upper 8.3 square miles of headwaters (5 linear miles of creek) from the lower drainage. Ten tributaries join the main stem of Novato Creek as it traverses the watershed below Stafford Dam. The lower Novato Creek watershed is well described by MCDPW11 and in in prior technical studies (KHE, 2014; Collins, 1998; Noble et al, 2005; Questa 2007; Royston Beck and Abby et al 1972).

Figure 2‐1: Novato Creek Watershed Topography and Drainages.

11 www.marinwatersheds.org/novato_creek.html

2‐3 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

This Hydraulic Study identifies and evaluates viable alternatives to improve flood and sediment management in the watershed. Current conditions in the corridor reflect ongoing urbanization in the watershed and management practices12 intended to reduce flooding by maximizing water and sediment conveyance within Novato’s creeks. Though successful in maximizing instream flows, identified ancillary impacts include: progressive channel incision (bed and bank scour) (Figure 2‐2) which increasingly require localized bank stabilization efforts; and channel maintenance dredging on a four year cycle to keep sediment scoured from upstream reaches from filling the bayland channel and obstructing creek drainage from the City into the baylands. The prior existing conditions assessment (KHE, 2014) and monitoring found that despite successful efforts to maximize flood conveyance with minimal out of channel flooding, both Novato Creek and Warner creek ycurrentl flow at or near bankfull downstream of Diablo Ave in a 10‐year event. Overbank flooding is predicted to be greater when the flood peak coincides with high tide. Because flooding is anticipated during large storm events, the Hydraulic Study also sought to identify and evaluate measures which reduce the adverse impacts of overbank flooding.

Figure 2‐2: Novato Creek Channel Incision (left) and Bayland Deposition (right)

12 Every four years, Marin County Flood Control Zone 1 dredges aggrading sediment between Diablo Ave. and the Sonoma Marin Area Rail Transit Bridge (SMART) to maintain channel conveyance in low lying reaches between Diablo Ave. and the Novato Baylands. In addition, routine channel maintenance in Novato Creek and its tributaries includes clearing downed trees, overgrown vegetation, and sediment blockages in the channel, and stabilization of failing banks.

2‐4 Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

2.2 Approach A Watershed Approach: The focus of the alternatives analysis is from Stafford Dam to San Pablo Bay including tributaries of Vineyard, Warner, Arroyo Avichi, Arroyo San Jose and Pacheco Creeks. In comparison with prior work, which focused on a selected reach or site, the Hydraulic Study looks more broadly at the entire watershed to identify opportunities for flood hazard mitigation both upstream and downstream of downtown Novato. This approach is necessary for the Novato watershed because flooding occurs as a result of overbank flows which originate both from upstream reaches and from tidal backwater which, during high tides, fills low lying reaches of Novato and Warner Creeks. The Hydraulic Study approach:

 Evaluates the impacts and recommends mitigation measures to maintain or improve the flood conveyance capacity now and in the future assuming that sea level rise and increasing storm intensity will increase watershed flood hazards;  Integrates consideration of riparian corridor as habitat for fish and wildlife, and identifies actions which concurrently support the ecological values of the watershed.  Considers geomorphic processes (sediment transport, deposition and scour) in the design and evaluation of flood mitigation in an effort to reduce channel maintenance costs and impacts;  Defines and evaluates measures to reduce the impacts associated with overbank flooding;  Evaluates tidal influences on low lying reaches of oNovat and Warner creeks below Seventh St./Tamalpais Ave.; and,  Evaluates actions in the tidal baylands to reduce dredge maintenance by expanding the creek corridor and restoring subsided tidal wetland to store aggrading sediment.

Consensus Based Alternative Development: Prior to modeling alternatives, KHE/MCDPW utilized a consensus approach to identify and select project alternatives. KHE defined a list of recommended project “elements” based on watershed assessment and existing conditions modeling. An “element’ is a group of actions which satisfy identified Hydraulic Study goals (e.g. building a spillway to reduce flooding in known location). KHE formulated a preliminary ranking criteria for the elements which considered flood control, implementation feasibility, ecological impact/benefit and cost. MCDPW conducted a series of stakeholder and public meetings to gather and integrate stakeholder input on the project elements and the ranking criteria. KHE used these tools to evaluate and rank identified elements, and created the short list of actions advanced for consideration in this study. Section 3 presents a description of the project elements and their ranking. KHE proposed three preliminary alternatives for stakeholder review. Stakeholders met four times in early 2015 to evaluate, modify and finalize the three (3) study alternatives. The alternatives are described in Section 4.

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Hydraulic Modeling, Refinement and Analysis of Alternatives KHE utilized the integrated watershed hydraulic models developed in prior study phases to evaluate the efficacy of the three alternatives13. Figure 2‐3 illustrates the boundaries of the integrated models. To evaluate alternatives, the numerical modeling team (KHE, WRECO, and DSI) modified the existing conditions models to reflect study alternatives. Alternatives are evaluated by comparing alternative flood impacts with those predicted by the existing conditions models. Storm drains are included in the analysis where the City of Novato’s Storm Drain Master Plan (in progress) study indicated these features are necessary for watershed flood impact assessment.14 The study utilizes 48‐hour (hr.) design storms associated with a 10‐year (yr.), 50‐yr. and 100‐yr. return periods. The effects of 12” and 36” of sea level rise (SLR) in San Pablo Bay are also evaluated for each

Figure 2‐3: Boundaries of the integrated models

13 In prior phases of this Novato Watershed Hydraulic Study (KHE, 2014), KHE configured and integrated four different numerical hydraulic models to simulate the volume and movement of both creek flow and overbank flooding from Stafford Dam to San Pablo Bay. The hydraulic models quantify rainfall‐runoff (HEC‐RAS) from the surrounding headwaters, non‐tidal instream and overbank flows and, where needed, storm drain flows (PC SWMM) on Novato and Warner Creeks. In reaches between Diablo Avenue and San Pablo Bay, a third model (EFDC) is used to characterize tidally influenced creek flows. This alternatives analysis utilizes these tools, in a comparative study to characterize the efficacy of elements based on the predicted change from existing conditions (EC). A detailed description of numerical model development and calibration are provided in the Hydraulic Assessment of Existing Site Conditions (KHE, 2014). Models were calibrated using USGS stream flow and Hydraulic Study monitoring data. 14 City of Novato’s independent Storm Drain master planning study served as the primary basis for determining the need for storm drain modeling. Data and analysis developed through the City study were generously provided and integrated into the Hydraulic Study.

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alternative. In final analysis, to facilitate planning and implementation, NPW modeled alternatives are organized into those elements recommended for action in the:

Short Term: Beneficial actions that can be constructed in 5‐10 year planning and implementation horizon. Medium Term: Beneficial actions that require additional studies, landowner coordination and possibly acquisition or easements to implement; and, Long Term: Beneficial actions to support long term adaption to increasing storm magnitudes and 1.5‐3 ft of sea level rise; including infrastructure relocation, modification and coastal retreat

WRECO led the creek modeling effort utilizing PCSWMM to evaluate changes in creek and overbank flooding. Figure 2‐4a illustrates the boundaries of the one‐ and two‐dimensional creek and channel models used to represent watershed conditions. In the tidally influenced bayland reaches, Dynamic Solutions International (DSI) led the bayland modeling effort which utilized a two‐dimensional model throughout the solution domain. Figure 2‐4b illustrates the boundaries, inflows and solution domain of the Hydraulic Study bayland model.

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Figure 2‐4: Boundaries and bathymetry (a. above) and model mesh (b. below) of the NHS Bayland Model

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3 STUDY ELEMENTS AND RANKING This chapter presents the process utilized for the identification and evaluation of project elements which are combined to formulate study alternatives.

3.1 Project Elements Determination Alternative development began with Phase I of the study, the Hydraulic Assessment of Existing Conditions (KHE, 2014). In this watershed‐wide hydraulic and geomorphic assessment, KHE integrated historical information synthesis, surveying, monitoring, site reconnaissance, mapping and numerical modeling of design storms from Stafford Dam to San Pablo Bay. Through this study, a suite of potential project elements were identified for consideration. An element is one or a group of actions, which when taken together result in a measure which provides a benefit consistent with project goals15. During the study, KHE refined these preliminary project elements to reflect new information gathered identifying physical watershed constraints and watershed management priorities for stakeholders. Elements were first refined through a collaborative process with the project’s primary stakeholders (Marin County Department of Public Works, City of Novato, the North Marin Water District, and the Novato Sanitary District). The Stakeholders participated in two internal working meetings, as well as providing individual review and additional supporting information. The revised elements were then circulated for review and comment from the broad group of participating stakeholders (Attachment A), and presented at a public Technical Working Group (TWG) meetings. In response, KHE further refined the elements, consolidating actions and disqualifying elements which do not address peak flood impacts16.

This process resulted in identification of fourteen (14) bayland elements and eight (8) creek elements. These elements, summarized in Table 3‐1, were agreed upon by stakeholders and anticipated17 to support the primary project goals stated above. Through the stakeholder process, study goals were further refined to focus on a reduction in community 50‐yr. flood risks, improvements in the efficiency of bayland sediment management, and measures to support climate change adaptation which anticipates both an increasing frequency of large storm events and sea level rise.

Elements retained in the final Alternatives assessment are presented in bold. Elements were removed from the study if they ranked low in the preliminary assessment, or if modeling analysis or ongoing engineering assessment determined the proposed actions did not provide measurable

15 For example, “Levee Removal” is an element which consists of excavation, hauling, and placement of material, and results in floodplain expansion. 16 This study focuses on peak floods and climate adaption. An equally important part of in‐stream habitat enhancement, which in not within the current study scope, is the evaluation and restoration of low flow habitat. 17Anticipated results are based on site assessment and existing conditions modeling.

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benefit, resulted in an increase in downstream flood depth or extent, or were deemed infeasible due to other infrastructural, operational or jurisdictional constraints.

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Table 3‐1: NHS Elements Summary (8 watershed/14 bayland) # CREEK Summary Element C‐1. Raise Stafford Action: Raise the crest of Stafford Dam 3 ft., creating an estimated 700 ac‐ft of storm water storage. Dam Spillway Modeling will assume Stafford Lake is full; and added storage is added behind the existing spillway crest. Crest Rationale: Added storage provides flood attenuation, lowering peak storm discharges downstream of the dam. C‐2. Modify Action: Modify the Stafford Dam tail water via modifications to the channel downstream of the outfall. Stafford Dam Analysis will increase in spillway energy loss and/or channel roughness/area. Tail Water Rationale: Tail water modifications will increase energy losses in an effort to reduce the downstream effects of the dam. Actions should decrease flows velocities downstream of the dam, and in turn, reduce scour and sediment transport capacity. C‐3. Restore Action: Restore tributary flood plain and modify tributary outfalls (Leveroni/Bowman/ storm drains to Floodplain discharge across available floodplain. Connect Novato Creek channel and floodplain on public parcels Upstream upstream and downstream of Bowman Canyon to increase the active flow area. Protect/expand riparian and/or corridora vi selective excavation along channel banks, and floodplain excavation and grading. Install large Downstream of wood grade control structures to reduce channel incision and support channel/floodplain connectivity. Bowman Rationale: Floodplain restoration provide flood attenuation in Q10 and lower storm events; and increases Canyon energy dissipation, sediment deposition and flood storage. Year‐round flood plain discharges support ground water recharge and increase summer base flows. Large wood structures work as energy dissipaters at high flows, and improve instream habitat during both high flows and low flows for resident steelhead. C‐4. Expand Novato Action: Expand narrowed channel cross section within available ROW via excavation of bedrock or layback of Creek Narrows banks. (Miwok to Rationale: Expanded channel cross section maintains conveyance and reduces backwater which contributes Pioneer park) to overbank flooding upstream of Simmonds Lane. Element analysis increases narrow channel cross sections (NOT to maintain channel geometry comparable to adjacent cross sections. SELECTED) NOT USED: This element was removed from consideration after hydraulic analysis indicated that adding conveyance at this location increased in the areal extent and depth of overbank flooding downstream. C‐5. Pico Vista Action: Direct overbank flows (from Novato Creek at Pico Vista) to Warner Creek via street and storm drain Surface Street routes to reduce flooding impacts. Modeling will evaluate flow conveyance requirements and downstream and Storm impacts associated with routing overbank water through a combination of street and storm drains. Drain Rationale: Local flooding can be reduced by modifying storm drains and sewer lines, surface streets, curb and Improvements gutter to accommodate a floodway. Measures reduces the impacts of overland flooding. (NOT NOT USED: This element was removed from consideration after hydraulic analysis and infrastructure SELECTED) assessment indicated that modifying conveyance at this location was limited to actions which did not significantly alter flood hydraulics. Implementation of floodway measures at this location should be evaluated with other sites in the future.

C‐6. Vineyard/War Action: Direct Vineyard/Warner Creek overbank flows in the vicinity of Center Rd and S. Novato Blvd., via ner Drainages streets and storm drains, to Scottsdale Marsh. Pump Nave Gardens storm water to Novato Creek. Route Surface Street street flows past Nave Gardens to Scottsdale Marsh & Storm Drain Rationale: Local flooding can be reduced by modifying storm drains and surface streets to accommodate a Improvements floodway. Routing flood water around the Novato Creek confluence increases available conveyance capacity for instream flows. Conveyance improvements reduce the duration and extent of flooding as well as storm water loading to sanitary sewer lines.

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Table 3‐1 continued: NHS Elements Summary # CREEK Summary Element C‐7. Increase Arroyo Action: Modify the Arroyo Avichi diversion structure to decrease volume of water and sediment being Avichi Diversion to directed into the Novato Creek confluence. Modify the downstream conveyance corridor (Novato Blvd Lynwood Basin Culvert, Baccaglio Basin, and conduit to Scottsdale Pond) to increase conveyance capacity via routes with existing storm drains and open channels. Rationale: Confluence area flooding can be reduced by directing a larger percentage of Arroyo Avichi flows downstream to Lynwood Basin. Routing flood water around the Novato Creek confluence increases available conveyance capacity for instream flows. C‐8 Expand Scottsdale Actions: Install a pump to increase conveyance from Scottsdale marsh to Lynwood basin. Excavate soils Marsh Storage within the Scottsdale marsh complex to increase the available storage volume and ponded open water area. Improve undersized conduit between basins to support increased storage and conveyance. Rationale: The addition of a pump permits discharge at high tide, increasing conveyance capacity through Scottsdale Pond, and a higher operational water level in Lynwood basin. Excavating within the marsh complex increases available detention storage. # Bayland Element Summary B‐1. Redesign Dredge Action: Modify the Novato Creek dredge channel geometry, to reduce the excavation extent, volume and Reach frequency while maintaining flood conveyance. Manage coarse sediment upstream of Baylands. Rationale: In 2016, Lower Novato Creek is scheduled for routine dredge maintenance requiring excavation and haul of 40‐60,000 cy of aggrading creek sediments. Site assessment modeling indicates that modifications to the dredge channel geometry that reduce the dredging footprint could be made while maintaining flood conveyance. A reduced excavation footprint may also increase sediment conveyance through the reach, yielding a longer project life. Upstream management of coarse sediment reduces costs management cost and bayland dredging. B‐2. Construct Spillway Action: Construct a spillway from Novato Creek to No. Deer Island Basin to increase floodplain conveyance, and Storm Water attenuate peak flood elevations and protect the SMART Bridge. Install culverts to provide gravity drainage of Basin for high flow floodwaters from No. DIB back to Novato Creek during low tides. Provide a secondary spillway/outfall to bypass to No. Deer central Deer Is. Basin. Island Basin Rationale: NoDiB provides flood storage not influenced by the tide which can be utilized when creek flood stages threaten community infrastructure. This “off channel” storage provides needed flood relief during high tides, and increases sediment conveyance in flood recession. The secondary discharge to central Deer Island basin increases capacity for peak flood conveyance, and limits flood stage in and around the storm water basin. B‐3. Remove South Action: Remove levees adjacent to Lynwood Basin (right bank) at Heron’s Beak and Duckbill Ponds. Relocate Levee at Duckbill upland fill material to a perimeter or setback levee within NoDIB or Lynwood Basin. and Herons Beak Rationale: In this un‐dredged reach, the available flow area is reduced by existing salt marsh. The heavily Ponds to expand vegetated marshplain and undersized channel reduces peak flows upstream, and downstream. Removing the the channel levees increases the available channel cross section by over 200%, improving flood and sediment conveyance. B‐4. HWY 37 Crossing: Action: Excavate channel and adjacent marshplain within the available Right of Way (ROW) to maximize the Expand Channel available channel cross section. in Available ROW Rationale: Creek conveyance is limited at Hwy 37, where three peered structures cross a narrowed Novato Creek. The adjacent floodplain grades up to meet the overpassing road. The efficacy of channel expansions in the upstream and downstream is limited by conveyance at this constrained location. Excavation to maximize the available flow area/conveyance capacity is warranted to provide peak flood drainage and sediment conveyance locally. Expanding the narrowed channel supports conveyance increases associated with upstream and downstream elements.

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Table 3‐1 continued: NHS Elements Summary # Bayland Summary Element B‐5. Construct Action: Construct culverts from Deer Island Basin South to West Basin, or a spillway from Novato Creek to Conduit from S. West Basin to expand the Novato Creek floodplain corridor width in the vicinity of Hwy 37. Construct outfall DIB to West culverts from West Basin to a downstream location Novato Creek, to permit drainage from West Basin during Basin to flood recession. increase Hwy Rationale: The channel geometry is restricted by existing structures, limiting water and sediment conveyance. 37 peak flood Increasing the available floodplain conveyance provides additional capacity during peak foods, increasing conveyance flood conveyance both locally and upstream. (NOT Not selected due to anticipated infrastructure constraints associated with conduit crossing both Hwy 37 and SELECTED) the recently Railroad ROW. B‐6. Direct Pacheco Action: Improve perimeter levees to preclude uncontrolled flooding to adjacent parcels. Construct spillway Pond peak from Pacheco pond to BMKV to direct discharge to points south when high tide/ flood waters in Novato Creek flood outflows preclude drainage. to BMKV Rationale: Pacheco Pond receives runoff from Arroyo San Jose and Pacheco Creek. During high tides, these outflows are stored in Pacheco Pond until tides fall on Novato Creek and allow accumulated water to discharge. During large storms the pond fills and floods adjacent lands. Levee improvements and an engineered spillway from Pacheco Pond to BMKV would reduce local upstream flooding. Another option (not modeled in this analysis) is an outfall from Pacheco Pond to the Hamilton Wetlands. The diversion reduces flood conveyance downstream to Novato creek, providing additional capacity for upstream inflows. In addition, directing Pacheco Pond outflows south at lower flows may increase upstream flood recession rates in Novato Creek, by diverting a significant volume of tributary water from the Novato Creek corridor. B‐7. Divide Action: Construct a new basin crossing level to divide Lynwood Basin into two parts. Construct new Lynwood Basin perimeter flood protection levees around the tidal portion of the basin. Install gated culverts in the new basin and add cross levee to permit gravity drainage of storm water from Lynwood Basin to Novato Creek at low tide. outfall(s) to Integrate these actions with the new pump at Scottsdale pond (Element C‐8). Novato Creek. Rationale: Dividing this large storm water detention basin increases its operational value. Currently, storm water from Scottsdale Pond drains to Lynwood Basin, and pumping is required to discharge to Novato Creek. Dividing the basin allows a portion of the volume to be open to tidal exchange, increasing tidal prism, and downstream channel geometry. The non‐tidal portion of the basin will continue to provide storm water detention storage downstream of Scottsdale pond. Multiple watershed alternatives increase the volume outflow being directed toward Lynwood Basin. Installing outfalls permits gravity drainage from the storm water basin when tidally influenced creek water levels drop below the basin WSE supports these upstream actions increasing storm water conveyance to Novato Creek. B‐8 Remove North Actions: Remove Levees separating Novato Creek (North Bank) from North Deer Island Basin (N. DIB). Bank Levees to Improve perimeter levees for coastal flood protection and modify perimeter drainage. Realign NSD primary Deer Island outfall crossing basin. Define, permit and implement an adaptive management plan to maintain flood Basin conveyance and wetland circulation in the aggrading basin. North/South Rationale: Expansion of the Novato Creek floodplain into N. Deer Island basin adds flood conveyance, sediment storage capacity and restores estuarine tidal wetlands. The added tidal exchange in the wetland increases the self‐sustaining channel geometry downstream, and reduces the need for downstream dredging. The available flood/marsh plain area provides capacity for natural geomorphic development of estuarine baylands both post construction and in the future in response to sea level rise. Rapid aggradation can be anticipated post construction, and local grading/hauling of some coarse sediment will be required to maintain creek conveyance during wetland development. Tidal wetland expansion in North basin supports an increase in downstream channel size and a geometry, reducing maintenance dredging needs in the Lower Novato Baylands.

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Table 3‐1 continued: NHS Elements Summary # Bayland Summary Element B‐9 Set Back North Actions: Set back levees along Novato Creek (North Bank) to expand Novato Creek floodplain and restore Bank Levees to estuarine wetlands between the NoDIB storm water basin and S. Deer Island Basin. Maintain a non‐tidal split Deer portion of North Deer Island Basin (No. DIB) to provide flood storage for Novato Creek during high tide. Island Basin Protect exist NSD force main, and maintain access for inspection. Improve perimeter levees/drainage to North support seasonal storm water storage. Rationale: Expansion of the Novato Creek floodplain into a portion of N. Deer Island basin adds flood conveyance, sediment storage capacity and restores estuarine tidal wetlands. The added conveyance capacity improves flood and sediment conveyance from upstream reaches daily, and during annual storm and peak flood events. The added tidal exchange in the wetland increases the self‐sustaining channel geometry downstream, and reduces the need for downstream dredging. Preserving a portion of the basin as non‐tidal maintains the opportunity for provide peak flood storage for downtown Novato during high tides. B‐10 Modify South Actions: Set back levees and relocate outfalls to increase downstream flood conveyance and recession. Deer Island Protect NSD force main. East of the NSD force main, if needed, provide additional wastewater Basin storage/disposal. levees/outfalls Rationale: Actions in this basin will vary by alternative in a manner consistent with actions proposed on adjacent parcels. Setting back the North bank levee increase floodplain area and reach conveyance. Levee improvements reduce flooding adjacent to Hwy 37 and NSD facilities. B‐11 Construct Actions: Construct spillway from Novato Creek to West Basin downstream of Hwy 37. If S.DIB floodplain is to Spillway and be inundated, construct culverts from S.DIB under Hwy 37/SMART to West Basin Construct outfalls from West Storm Water Basin to Novato Creek to permit floodplain recession via gravity drainage. Modify NSD spray irrigation Basin for high facilities to permit summer operations and facilities removal during flood seasons. flow bypass to Rationale: The channel and floodplain constrictions at Hwy 37 reduce upstream flood conveyance and is a West Basin source of local flooding. A spillway to West Basin downstream of Hwy 37 will provide additional flood (NOT storage, and increase Hwy 37 flood protection by slowing the rise water levels in the vicinity of the structure. SELECTED) Culverts from S. DIB to West Basin provide a relief valve when flood waters and debris are detained behind the structure. Added floodplain storage extends the duration of flood recession, and increase bayward sediment transport. Seasonal operation of NSD spray irrigation facilities permits dual use of the basin. This element was replaced with Element B‐12, following initial modeling and cost analysis, and NSD agreement. B‐12 Restore Tidal Actions: Relocate or reconfigure NSD spray disposal capacity. Set back perimeter levees along Hwy 37 in an Floodplain to alignment that protects NSD force main. Excavate a new primary creek channel alignment reducing creek West Basin sinuosity, and directing high velocity flows downstream and away from BMK homes. Remove perimeter Oxbow levees and design restored tidal floodplain with consideration of Pacheco Pond circulation and drainage. Rationale: Restoration of tidal floodplain expands the available channel cross section for flood and sediment conveyance. Tidal wetland restoration increases bayland tidal exchange, and the associated stable channel dimensions reducing downstream dredging requirements. Excavation of a new primary creek channel alignment supports increased flow conveyance without increasing scour and marsh loss along the existing channel alignment. Shallow grading to focus floodplain conveyance improves intertidal flow across the marsh plain, increases sediment deposition and accelerates wetland formation.

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Table 3‐1 continued: NHS Elements Summary

# Bayland Summary Element B‐14 Restore East Actions: Relocate NSD summer disposal capacity to perimeter lateral outfall. Remove levees separating Basin to Tidal Novato Creek (north bank) and Simmonds Slough (north bank) from East Basin. Construct marsh plain and Wetlands shallow interior pilot channels. Improve perimeter levees and drainages along Hwy 37, perimeter uplands to the east, and the west bank of Simmonds Slough. Relocate Simmonds Slough pump station to Hwy 37. Rationale: Setback of flood control levees will restore of 480 acres of tidal baylands which serve as available floodplain increasing flood conveyance during low tide storm events. Habitat restoration supports regional recovery rplans fo special status species. During all tides, the deeply subsided baylands provide depositional areas for Novato Creek sediments and room for changing depositional patterns which support natural bayland adaption to sea level rise. The increase in tidal exchange supports a larger Lower Novato channel cross section and thereby reducing the need for maintenance dredging. Interior channels support subtidal habitat, and guide tidal circulation and sediment movement in the restored wetland. Managed retreat of levee and pumps reduce community infrastructure and increase operational efficiency.

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3.2 Project Elements Evaluation: The Criteria Development and Ranking Process Criteria Development: To support element refinement, stakeholder valuation, and consensus in developing alternatives, KHE defined evaluation criteria reflective of project goals, and a scoring system to rank how each element satisfies a given criteria. The project elements, evaluation criteria and ranking are presented for bayland and creek elements in Table 3‐2 and Table 3‐3. Attachment C presents a description of the element ranking criteria used in these tables. The evaluation criteria are subdivided into three categories ‐ flood control, ecological, and implementation feasibility. The Hydraulic Study team and stakeholders reviewed, evaluated and modified these criteria concurrently with the review of project elements.

Within the proposed element tables, stakeholders used a ranking system to rate how each element satisfies a given criteria. Scores range from ‐2.0 to +2.0. A value of +2 is the highest score with respect to an element achieving or improving a given criteria, and ‐2 scores the least desirable outcome with respect to a given criteria. A value of 0 indicates an element with no positive or negative impact in a criteria category. The tables also utilize an element weighting factor to allow stakeholders to modify criteria weighting to reflect their organizational priorities. Setting this multiplier to a value of 1 results in equal weighting for all criteria. The score for each element is the total of all criteria rankings. At the request of stakeholders, KHE added to the table category wide weighting factors to indicate relative priorities between criteria, and score subtotals for each group of criteria. The element ranking was taken as the simple total of all stakeholder weighted scores, with the highest score indicating the highest ranking.

In addition to scoring, KHE developed preliminary capital cost estimates and the percentage changes to operations and maintenance obligations. These preliminary cost ranges were presented for comparative purposes to provide an indication of the relative costs between elements18.

18 Design costs may vary significantly depending on the elements selected and construction phasing. Note: These costs are superseded by more detailed cost estimates prepared for elements selected for final analysis.

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Table 3‐2: Novato Bayland Alternative Elements and Ranking Criteria

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Table 3‐2 continued: Novato Bayland Alternative Elements and Ranking Criteria

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Table 3‐2 continued: Novato Bayland Alternative Elements and Ranking Criteria

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Table 3‐3: Novato Creek Alternative Elements and Ranking Criteria

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Element Ranking: Working with project Stakeholders, KHE prepared the ranking Tables 3‐2 and 3‐3. Stakeholders collaborated in iterative review to integrate individual priorities and to refine the overall ranking. The element ranking process began with a public meeting to review preliminary elements (identified by KHE in prior phases), proposed criteria and ranking approach. In response to this review, KHE modified and grouped some elements, and organized the elements sequentially from headwaters to bay. Stakeholders met a second time to review the revised tables and preliminary ranking, and to discuss modifications to the rankings. KHE incorporated those comments and circulated the tables as spreadsheets to provide stakeholders an opportunity to play with weighting factors and scores as part of the evaluation of the ranked elements. A third meeting was held providing an opportunity for group review following incorporation of this second set of comments19.

Stakeholder collaboration in the ranking process provided opportunity for discussion regarding priorities, synergies and obstacles associated with the element implementation. During element review, stakeholders agreed to remove from the analysis those elements which were not, as independent actions, expected to improve flood control performance during peak (50‐yr storm) events. These elements, summarized in Table 3‐4, will not be evaluated further in this hydraulic modeling study. However, they are an important part of the overall approach for watershed management. Recommended bayland and creek actions that will not be modeled include: source/in‐stream management of coarse sediment; bayland ecological enhancements to support special status species and integrating waste‐water reuse in bayland planning20.

19 The final elements ranking tables have criteria weighting set to 1 (unused). Stakeholders modified the weights in the ranking process, but found that weighting was not needed to develop consensus on a final ranking. 20 Hydraulic Study wetland restoration concepts define and evaluate general breach, channel and levee configurations, but do not provide detailed wetland restoration design for individual basins or wastewater discharge modifications. 3‐13

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Table 3‐4: Element Recommendations Not Modeled

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Table 3 ‐4 continued: Element Recommendations Not Modeled

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4 STUDY ALTERNATIVES

4.0 Study Alternatives Overview: The goals of the Hydraulic Study are: 1) to develop a suite of predictive numerical models to characterize hydraulics, evaluate sediment conveyance capacity in the watershed; and 2) identify and group a suite of potential actions into three alternatives to reduce community flood risk, improve the efficiency of sediment management, and improve instream habitat. These goals require determination of alternatives which improve operational efficiency, and reduce ecological impact associated with flood control operations, on‐going watershed scour and bayland sediment aggradation.

The Hydraulic Study began by evaluating three alternatives modifying bayland (tidally influenced) hydraulics, and three alternatives modifying creek (non‐tidal) hydraulics. Final analysis combines bayland and creek alternatives to assess changes in flood hydraulics from Stafford Dam to the Novato Bayland terminus at San Pablo Bay. An Alternative is a grouping of elements selected to provide a desired improvement in flood and resource management within the watershed. The overarching goal of the NPW study is to reduce peak flood water surface elevations, and increase flood and sediment conveyance through the dredged reach, while improving ecological conditions in the corridor. Recommended alternatives reflect the Hydraulic Study team’s understanding of current (or existing conditions) flood hydraulics across the watershed and baylands as characterized by flow monitoring, watershed and geomorphic field assessment, and calibrated numerical models developed for this project in Phase II.

Creek alternatives developed for this study reduce flooding by: 1) adding storage or reducing flood/sediment conveyance upstream of Sutro Ave.; 2) improving conveyance both within Novato and Warner Creeks; and 3) improving conveyance in areas of overbank flooding. Baylands alternatives expand the currently leveed floodplain via spillways for storm water or breaching (levee removal) to tidal basins adjacent to Novato Creek. These actions reduce both peak flood water surface elevations (WSEs) and daily high tides. Evaluation of creek and bayland actions together is necessary for the Hydraulic Study because the City of Novato is susceptible to flooding from watershed runoff (upstream), which is made worse by high tides (downstream) that reduce City drainage capacity. As a result, actions are required to address flooding in Novato from both upstream and downstream sources.

In a preliminary analysis, KHE grouped stakeholder selected elements based on physical processes (e.g. storage and conveyance) and functions (e.g. sediment management, flow diversion, or channel maintenance). This preliminary analysis informed the Hydraulic Study team regarding watershed response to hydraulic modification. Extensive model refinement and revision was undertaken to

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accurately characterize existing condition and refine elements which yielded hydraulic improvements in flood. These concepts are intended to support long term planning, as well and engineering design, environmental compliance and permitting for short term actions.

Each of the recommended study alternatives (Short, Medium and Long) creates an incremental decrease in peak flood water surface elevation or increases conveyance capacity within the creek and/or bayland as compared to existing conditions. In urban areas, a change in impact is measured by a change in the overbank depth of flooding and/or the number of buildings impacted on the flood plain. Measures which reduce peak flow or velocities in the creek channel (thereby slowing ongoing bed/bank scour) or increase flood recession rates (thereby decreasing the duration of flooding) are also considered favorable. In the baylands, reductions in peak flood WSE and increases in bayward flow and velocity are presented as indicators of benefit.

4.1 Short Term Alternative Elements: The Short Term Alternative consists of those actions that can be constructed in 5‐10 year planning and implementation horizon. Figure 4‐1 maps the elements (described in Section 3) and depicted in Figures 4.1b and 4.1c which make up the Short Term Alternative. The elements and their estimated costs are presented in Tables 4.1 and summarized briefly below. Hydraulic analysis results presented in Section 5 serve as the basis for the elements recommended as a priority for implementation shown in bold text below.

. Restoration of the Leveroni Creek Tributary Floodplain: Tributary floodplain restoration redirects the tributary creek inflow across available floodplain downstream of Stafford Dam. Changes to the outfall and grading on the floodplain disperse and store water and sediment, releasing it more slowly to the Novato Creek channel21. To the extent possible, this element should be expanded to encompass Novato Creek floodplain

. Install Storm Drain Flap Gates in Tidal Reaches This element reduces flooding by keeping creeks from backing up into low lying streets (downstream of Seventh St/Tamalpais Ave., and along Center Rd. and S. Novato Blvd.) in storm events with concurrent high tides.

21 More expansive floodplain restoration initially considered in the Short Term Alternative, was deferred to medium and long term alternatives because analysis indicated that these elements reduced flooding in the upper watershed, but the reduction in upstream flooding increased flooding downstream. Similarly, actions to improve Novato Creek channel conveyance near Miwok Park and Pico Vista were removed from the Short Term Action Alternative because analysis indicated that while a local flood reduction benefits could be obtained, it yielded an increase in flooding downstream in the watershed.

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. Increase Arroyo Avichi Diversions to Lynwood Basin. This element in the Lower Warner Creek drainage increases the percentage of Arroyo Avichi flow diverted to Lynwood Basin via Scottsdale Marsh by modifying an existing diversion weir and downstream storm water drainage infrastructure to and through Scottsdale Marsh. Diversion of Arroyo flows around the Novato/Warner Creek confluence creates added capacity for upstream inflows, and reduces the sediment loading to the aggrading dredge reach.

. Increase Scottsdale Pond Storm Water Conveyance to Lynwood Basin This element adds a pump at Scottsdale pond to improve conveyance to Lynwood Basin. During large storm events, the pump adds storm water drainage capacity in low lying areas or the Warner Creek drainage, and supports increased Arroyo Avichi discharges22. In Lynwood Basin conveyance to Novato Creek is increased by adding culverts which provide gravity drainage of storm water at low tide.

. Redesign of the Dredge Reach: This element modifies the extent and footprint of channel maintenance dredging between Diablo Ave and the SMART Bridge to one that is more self‐sustaining, reducing the impact and cost of dredging. Modification to the dredge profile reduces the excavation volume based on geomorphic characteristics to establish a more stable (less rapidly aggrading) channel geometry to reduce sedimentation rates without loss of upstream flood conveyance capacity.

. Spillway and Storm Water Basin for High Flow Bypass at N. Deer Island Basin: This new northern storm water basin with a flood spillway are constructed at North Deer Island Basin to improve City drainage during concurrent peak floods and high tides. The spillway provides a secondary route for storm water discharge when conveyance is reduced on Novato Creek during high tides.

. Remove/Relocate Novato Creek Levees Four elements are combined to expand the Novato Creek channel, increase flood conveyance and provide additional sediment storage capacity. The levees removed along the south bank of Novato Creek upstream of Hwy 37 add conveyance and sediment storage capacity to the narrow channel downstream of the actively dredged reach.

22 Coarse sediment which reaches the new bayland basin in high flows will not be transported downstream at lower flow regimes. The basin can be expected to aggrade over time. Therefore, source control actions to reduce coarse sediment loading from upstream of the bayland are also recommended. 4‐3

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. Divide Lynwood Basin to add a tidal exchange and sediment storage at the upstream limit of the bayland. The new Lynwood tidal basin adds tidal prism (daily tidal exchange volume)23 to sustain the expanded creek channel geometry post construction. The new tidal basin increases sediment storage capacity, and allows sediment to disperse over a broader area, which reduces upstream channel aggradation and extends dredging cycles.

. Reconfigure Levees at West Basin Oxbow setting back levee along the north bank of Novato creek to restore floodplain and add a tidal exchange in the middle of the bayland. Hydraulic modeling indicates that reconnecting this subsided basin increases flood attenuation downstream of the Hwy 37 bridges, and reduces local ebb and flood velocities to promote sediment deposition. Realignment of the Novato Creek thalweg reduces flood epressur on Novato Creek banks at BMK. The associated increase in wetland tidal prism sustains a larger tidal channel cross section, reducing bayward maintenance dredging. The large low velocity basin supports bay and creek sourced sedimentation.

23 Tidal Prism definition and value for channel maintenance 4‐4

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Table 4‐1: Novato Creek Elements in the Short Term Alternative

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Figure 4‐1: Short‐Term Alternative Elements

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Figure 4‐1a: Short Term Element 3, Restoration of Leveroni Creek Tributary Floodplain

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Figure 4‐1b: Short Term Elements 5‐6

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Element Short Term

Install Flap Gates on Pipes within Nave Gardens. Install Flap 7 Gates on Center Road Pipes to Warner Creek.

Increase Arroyo Avichi Diversion to Lynwood Basin. Increase 8 conveyance in Novato Blvd Culvert, Baccaglio Basin, Scottsdale Pond. Install pump at Scottsdale Marsh to Lynwood Basin. Increase 9 conveyance out of Baccaglio Basin.

Figure 4‐1c: Short Term Elements 7 through 9

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Figure 4‐1d: Short Term Alternative Elements in the Baylands 4‐10

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4.2 Medium Term Alternative: Medium Term elements are those that can be implemented in a 10‐15 year time frame. Medium Term elements continue the Hydraulic Study efforts to increase flood storage and conveyance capacity in both creek and bayland corridors. Implementation of these actions requires additional study, landowner coordination and possibly acquisition or easements. The elements that make up the Medium Term Alternative are described in Section 3 and shown in Figures 4.2b and 4.2c. The elements and their estimated costs are presented in Table 4‐2 and summarized briefly below. Hydraulic analysis results presented in Section 5 indicate that implementation of these actions further reduces peak flood water levels in both creek and bayland reaches.

. Raising Stafford Dam: The Stafford Dam crest elevation is increased by 3 ft, creating an additional 700 ac‐ft of storage. Improvements to the Stafford Dam tail water are also incorporated to dissipate energy increases immediately downstream of the modified structure. Hydraulic modeling indicates that increasing dam storage in combination with Bowman Canyon floodplain restoration provide the greatest downstream flood benefit.

. Restoration of the Bowman Creek Tributary Floodplain: Tributary floodplain restoration redirects the tributary creek inflow across available Bowman Creek floodplain. Like Leveroni Creek, this element attenuates tributary inflows, and reduces sediment loading to upper Novato Creek by routing the creek across a modified flood plain. Floodplain restoration increases groundwater recharge which supports summer base flows critical to support fish and aquatic habitat.

. Lower Warner Creek Drainage Improvements: This location is an ongoing focus of work because much of the overbank flows upstream consolidate in this low lying area. Two elements are considered. At Scottsdale Marsh, storm drain improvements expand undersized conduit to increasing conveyance within the Marsh. Earthwork, including excavation provides additional open water storage areas expanding Scottsdale Pond. In the Nave Gardens neighborhood, installation of pa pum provides local storm water drainage when creek stage rises above the elevation of storm drain outfalls.

. Split North Deer Island Basin: Set back levees on the north side of Novato Creek, expanding upper Novato Creek and splitting North Deer Island Basin (NoDIB). Setting back levees adds another large tidal basin to support bayward sediment transport and aggradation. The new levee configuration retains seasonal wetland north of the expanded bayland channel providing storm water storage in peak flood conditions.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

. Expand Novato Creek Channel at Hwy 37: Excavate marshplain and channel between existing levees to increase the available flow area at a known bottleneck. Modeling indicates that expanding this channel constriction improves conveyance both upstream and downstream. Elements include raising levees at S. Deer Island Basin (S. DIB) and Lynwood Basin to reduce/constrain flooding along the Hwy 37 corridor. Increases in upstream tidal prism associated with upper bayland levee realignment are anticipated to maintain the enlarged cross section post construction.

. Raise Pacheco Pond Perimeter Levees and Discharge in Flood to BMK Restoration Site: Raise northern and southern levees to a consistent elevation, and install a flood spillway or culvert to the BMK Restoration Site. These infrastructure improvements limit peak flood water levels in and around the pond to reduce perimeter flooding, and constrain/direct overtopping flows to the BMK restoration site and away from Novato Creek. Outfall design and hydrologic connectivity should be integrated with BMK Restoration actions.

. Relocate Bayland Infrastructure and Breach Levees to Return East Basin to Tidal Baylands: Construct a new coastal flood protection levees along Hwy 37 and the adjacent upland margin. Set back the Simmonds Slough pump(s) and Novato Sanitary District (NSD) facilities as part of the managed retreat to a new bayland boundary. Grade site interior to support modification to waste/storm water discharges and enhance ecological values. Breach East Basin levees to convert the subsided basin to tidal bayland, accelerate flood recession and increase tidal prism to expand the natural geometry of Novato Creek at the confluence with San Pablo Bay. Given the numerous many actions under consideration in the watershed, transfer of property ownership and implementation of the East Basin restoration actions to a state or federal bayland resource management agency is warranted.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Table 4‐2: Novato Creek Elements in the Medium Term Alternative

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 4‐2: Medium‐Term Alternative Elements 4‐14

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 4‐2a: Medium Term Alternative Upper Creek Elements:

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Added Nave Gardens Pump and Increase Scottsdale Pond Storage

Stafford Dam: Raise Spillway Crest and Increase Energy Dissipation Immediately Downstream

Figure 4‐2b: Medium Term Alternative Creek Elements Continued

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 4‐2c: Medium Term Implementation Elements Upstream of Hwy 37 4‐17

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 4‐2d: Medium Term Implementation Elements Downstream of Hwy 37 4‐18

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

4.3 Long Term Alternative Elements: Long Term elements are those that can be implemented in a 20+ year time frame to support long term adaption to increasing storm magnitudes and sea level rise. Long term actions in the Novato’s creek corridors expand medium term work in upper watershed floodplain restoration, and lower watershed storm drain and surface street improvements. In the Bayland, long term actions relocate much of the remaining Novato Bayland flood control infrastructure to the upland perimeter, while maintaining coastal flood protection for Hwy 37 and the recently improved railroad ROW. The elements that make up the Long Term Alternative are described in Section 3 and shown in Figure 4‐ 3. The elements and their estimated costs are presented in Table 4‐3 and summarized briefly below. Hydraulic analysis results presented in Section 5 indicate that implementation of these actions, in addition to the Short Term and Medium Term Alternative actions, presented in Sections 4.1 and 4.2, further reduce peak flooding in both creek and bayland reaches of Novato Watershed creeks.

. Restoration of the Novato Creek Floodplain at O’Hair Park: Long term actions expand upper Novato Creek floodplain restoration to creek‐side parcels within O’Hair Park increasing connectivity between Novato Creek and its floodplain. Allowing flows to expand across floodplain slows creek velocities and decreases scour and sediment conveyance downstream. The benefits of floodplain restoration increase with available area and connectivity with the low flow channel. The addition of Novato Creek flood plain restoration at O’Hair Park compliments tributary flood plain restoration elements associated with Short and Medium term alternatives.

. Lower Warner Cr. Drainage Improvements: Surface streets, storm drain and sanitary line improvements are extended north along S. Novato Blvd. to between Tamalpais Ave. and Scottsdale Pond to reduce the impacts of overbank flooding both locally and from upstream sources. This creates a route (or “floodway”) for overbank flood water management during large storm events. These improvements do not reduce the volume of flooding. They are intended to decrease the footprint and/or impact of flooding by consolidating and managing flood waters along improved routes which accelerate flood recession and reduce the duration of flooding.

. Restore Tidal Bayland at North and South Deer Island Basins Relocate flood control levees in Deer Island basin to the upland perimeter and restore tidal exchange to the Deer Island central basin. These actions maximize tidal exchange in the bayland, and flood attenuation in upstream creeks. Benefits associated with peak WSE decrease will be lost over time to sea level rise. Actions eliminate storm water storage capacity in the central Deer Island basin, limiting the available storm water storage volume. Implementation requires: realignment of NSD primary outfall and/or conversion to lateral 4‐19

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

discharges along the basin perimeter to accommodate levee realignment, and perimeter infrastructure modification to accommodate tidal and sea level rise driven increases in outfall elevations. Because flood attenuation benefits are lost over time to SLR, final levee alignment and the balance of land use between tidal exchange and storm water storage should be re‐evaluated as future tide/flood conditions change.

. Remove Remnant East Basin Levees Remove upland fill from the restored bayland and reuse the material to support ongoing infrastructure improvements in Novato Baylands. Due to increasing demand, future projects are expected to be material limited. Remnant east basin upland fill can be progressively removed for beneficial reuse, and/or to provide mitigation for ongoing bayland flood management and/or maintenance actions. To reduce long term maintenance obligations and costs, transfer of property ownership and implementation of the East Basin restoration actions to a state or federal bayland resource management agency is warranted.

Table 4‐3: Novato Creek Elements in the Long Term Alternative

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 4‐3: Long‐Term Alternative Elements 4‐21

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 4‐3a: Long Term Implementation Elements Upstream and Near Hwy 37

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 4‐3b: Long Term Implementation Elements Downstream of Hwy 37 4‐23

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

5 Alternatives Analysis This study utilizes hydrology and hydraulic computer models to evaluate the efficacy of alternatives based on the change in conditions from those predicted for existing conditions in the watershed and efficacy in meeting project goals described in Section 2, and utilized as the basis for element selection and ranking (Section 3: Tables 3.1 and 3.2). In the urbanized Creek corridor, the analysis considers the reduction in maximum water surface elevation. Changes in the extent of flooding are depicted on plan maps, and quantified based on the number of buildings impacted. In the largely undeveloped baylands, the analysis looks at the change in flood WSE maxima and the location of flooded areas. The Bayland analysis also evaluates the change in the water surface gradients during flooding and flood recession. These gradients drive the transport of water and sediment into and across the baylands. Flow velocity profiles and shear stress maps were evaluated as measures of the resulting change in sediment transport capacity and flood recession rate across the baylands.

Hydraulic modeling analysis evaluated the performance of each set of alternatives using the 14 design storm (inflow) and tidal boundary conditions scenarios presented in Table 5‐1. The analysis considers three flood flow regimes, Q10, Q50 and Q100. To be conservative, the Hydraulic Study assumes that a San Pablo Bay mean higher high water (6.5 ft, NAVD88) occurs at approximately the same time as the peak storm discharge. After review of preliminary modeling results, the study team selected the suite of scenarios identified in Table 5‐1 to provide a range of conditions over which to evaluate study alternatives1. Table 5‐1: Alternatives Analysis Scenarios: Alternatives Analysis Scenarios (# of Scenarios) Existing Conditions Q50, Q50+1ftSLR, Q50+3ftSLR (8) Q10, Q10+1ftSLR Q100 Q50(mid‐tide), Q50(mid‐tide)+3ftSLR Short Term Q50, Q50+1ftSLR, Q50+3ftSLR Q10+1ftSLR (7) Q100 Q50(mid‐tide), Q50(mid‐tide)+3ftSLR Medium Term Q50, Q50+3ftSLR (3) Q10+1ftSLR Long Term Q50, Q50+3ftSLR (4) Q100 Q50(mid‐tide), Q50(mid‐tide)+3ftSLR

1 Results for Q10 design storm conditions were generally comparable with both the MHHW and MHHW+1 ft boundary condition. The MHHW+1 ft boundary conditions, which approximates future SLR condition as well as current storm and King tides observed during the study monitoring periods , was utilized for Q10 analysis. 5‐1

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

A summary of observations and conclusions based on final modeling results are presented below. Compilations of Creek and Bay model results are provided in Attachments D and E, which contain plan maps of peak WSEs and time series of stage, discharge and velocity at selected locations throughout the watershed. Design storm (Q10/Q50/Q100) modeling results for each Alternative (Short Term, Medium Term, and Long Term) are presented below, followed by discussion of changes associate with SLR scenarios and mid‐tide analysis.

5.1 Alternatives Analysis of Design Scenario General Watershed Observations: Upstream of the baylands, maximum flood WSEs are reduced along the Novato Creek and Warner Creek corridors (due to upstream changes), and in low lying areas which accumulate overbank flows from upstream and/or benefit from WSE reductions created by bayland actions. In general, elements upstream of Simmons Lane provide a localized flood benefit. However, in the absence of added storage (like that provided by raising Stafford Dam), the reduction in overbank flooding upstream of Simmonds Lane conveyed more water downstream and resulted in an incremental downstream shift in flooding. This unfavorable result occurs during the large design storm events because urbanized reaches of Novato and Warner Creeks flow at or above capacity in large storm events and during high tides.

Alternatives analysis results for Novato and Warner Creek reaches for Q10/Q50/Q100 analysis are presented in Tables 5‐1 through 5‐3.

In the baylands, maximum flood WSEs are decreased by reconnecting adjacent baylands via levee breaches or removal to provide additional natural functioning marshplain storage capacity (tidal prism), and expand available flood plain within the restored marshes which accelerates flood wave attenuation. Because of the existing long, narrow geometry of the Novato Baylands, restoration of tidal floodplain also reduces the amplitude of the daily tide range, creating the added benefit of lowering the starting water surface elevation in the baylands. This occurs because the time required to fill the large subsided basins increases with storage volume. As a result, the basins do not fill completely during flood periods. The result is a reduction in the maximum water levels in both the creek and the basin, and an increase in the available tidal basin storage capacity. This benefit is greatest relative to current existing conditions, but decreases with SLR. Bayland peak flood water surface elevation reductions for design storm events are presented in Table 5‐4.

Short Term Alternative Analysis (Table 4.1 presents a summary of Short Term Elements which are mapped in Figure 4.1.) Analysis results are presented in a general order from headwaters to bay.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

As noted above, in the upper watershed the Short Term Alternative creek actions intended to increase conveyance have limited benefit at higher flows because Novato and Warner Creeks are already flowing at or above capacity in the lower watershed. Elements which were initially proposed to increase creek conveyance and reduce overbank flooding upstream of Simmonds Ln., also had an adverse impact in that they translated flooding downstream. These elements (upper creek floodplain restoration, expansion of the channel cross section and Miwok narrows, and decreasing overbank flows at Pico Vista Lane) were removed from the Short Term Alternative following preliminary analysis2 because mitigations could not be found to ameliorate the downstream impact3. As a result, there is only one Short Term element upstream of Grant Ave., the Leveroni Tributary floodplain restoration. This small scale upper Novato Creek floodplain restoration does not significantly reduce peak flood WSEs either locally or downstream during the large design storm events. Despite this lack of efficacy in peak flood, retaining this and other flood plain restoration elements are warranted to provide ecological benefits at lower (inter‐annual) flow magnitudes, and to support higher base flows during dry season conditions.

Upstream of the Baylands, Figures 5‐1 through 5‐3 present the predicted existing conditions and the change in floodplain inundation depth associated with the Short Term Alternative for Q10, Q50 and Q100 events. In general, benefits of short term actions upstream of the baylands, occur primarily downstream of Diablo Ave., with the greatest benefits associated with Lower Warner Creek drainage diversions, and Bayland actions (discussed below) which create WSE reductions in and adjacent to the Novato/ Warner Creek confluence. Lower Warner Creek drainage elements improve storm conveyance from Diablo Ave to Lynwood Basin, but only lower water level maxima slightly upstream of the confluence reach. This occurs because the added conveyance in the more downstream reaches of the watershed draw more water from inundated areas upstream. Overall, the Short Term Alternative creates a 13% reduction in the number of structures impacted at Q10. The benefits at Q50/Q100 were nominal; only a 1% reduction in buildings impacted was achieved. Despite the limited benefit, these actions warrant ongoing consideration because they allow flood waters to pass more efficiently through the corridor, reducing the duration of flooding during large events.

For the Baylands and tidally influence reaches up stream, Table 5.4 and Figure 5.4 summarize the change in bayland Short Term peak WSEs between Diablo Ave and San Pablo Bay. Peak flood WSEs

2 During creek modeling and analysis, the study team modified element configurations and combinations multiple times in an effort to identify measures which would provide a downstream benefit without increasing flooding in other locations in the corridor. 3 The increase in storage provided by Stafford Dam in the Medium Term Alternative provides this capacity, increasing opportunities for improved flood management downstream.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

decrease rapidly through the confluence reach producing 1‐3 feet of flood reduction. In comparison to existing conditions, typical water surface elevation maxima decreases of 2‐3 feet at Q10 and 1‐2 feet at Q50/100 in the upper bayland. An equally important benefit to short term actions is the consistent bayward gradient (slope) which extends beyond Nave Gardens to the SMART station before flattening across the expanded channel at No. Deer Island Basin. The downstream extension of the higher bayward gradient supports a higher sediment transport capacity through the dredged reached. The flattening of the water surface slope indicates the transition from transport to deposition dominated which the Short Term alternative shifts downstream from the dredge reach into the expanded bayland corridor where additional channel capacity is proposed to increase downstream conveyance. Medium and Long term actions increasingly expand intertidal area providing room for sediment storage and expansion of tidal wetland ecotones.

Downstream of Hwy 37, Short term peak flood stage decreases get smaller with distance downstream at Q10, becoming negligible downstream of the BMK North Lock. At Q50/Q100 the WSE reductions associated with Short Term Actions reach only as far as Pacheco pond. Peak flood WSEs are comparable or slightly (0.25 ft.) higher than existing conditions further downstream. This small increase is likely due to the added upstream conveyance, and is expected to be mitigated by natural geomorphic downstream channel adjustment. This is a small adverse impact is likely to be temporary, but should be further evaluated in design.

In addition to reducing flood maxima, the Short Term alternative decreases the flooded area associated with design storm. Figures 5.5 through 5.7 map maximum Q10, Q50 and Q100 flood elevations. Existing (a) and Short Term Alternative (b) conditions are presented as upper and lower left maps respective; the right map illustrates the predicted change (Existing minus Short (c)) in WSE maxima . Short term actions decrease peak flood water surface elevations from Diablo Ave. to upstream of Hwy 37. Short term actions decrease, but do not eliminate, flooding around Hwy 37, Pacheco Pond and in the BMK North Lagoon. Levee setbacks at West Basin do not results in a significant decrease in WSE in peak flood. Modeling results for Short and Medium Alternatives suggests this the due to both the upstream conveyance constriction at Hwy 37, and added outflows from Pacheco Pond. Benefits are comparable at Q10 and Q50/100. It is notable that at Q50, isolated flooding occurs at Montego Key Park in Bel Marin Keys because it is lower than adjacent parcels. Local ground improvements are recommended to raise this parcel to that of surrounding grades.

Predicted changes in peak flood velocities associated with the Short Term Alternative are summarized in Table 5.5 and plotted in Figure 5.8 and 5.9. At Q50 and Q100 flows, the Short Term Alternative increases bayward velocities from Diablo Ave. to and downstream of no. Deer Island Basin. Velocities decrease at Deer Island Basin as flows transition into the expanded channel cross section. Q50 and Q100 channel velocities are comparable because Novato Creek flows at and above

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

bankfull channel capacity during both events. This trend is consistent for all design storms and Alternative scenarios. In the Q10 scenario, predicted velocities upstream of Hwy 37 are 0.5‐1 ft/sec lower than predicted by the existing conditions model. The diversion of Arroyo Avichi flows from the Novato Creek confluence lowers downstream flow velocities at Nave Gardens. Further downstream the increase in channel cross section decreases Novato Creek velocities through the upper bayland. Figure 5.9 presents Predicted bed shear stress, a velocity driven measure of bayland sediment transport capacity. As documented in the existing conditions report (KHE, 2014, Section 3.3.2), to initiate movement of fine gravel typically requires shear stress values of greater than 5 N/m^2. Predicted shear stress values at or above this threshold are mapped as red in Figure 5.9. The Short Term Alternative scenario maintains higher shear stress between Hwy 101 and No. Deer Island Basin indicating an increase in sediment transport capacity within the dredge reach. The rapid transition to low shear values within the Upper Bayland indicate the Short Term Alternative would shift sediment deposition downstream toward the expanded Upper Bayland cross section. Since velocity decreases with increasing flow area, the tidal portion of Lynwood Basin is anticipated to have the highest sedimentation rates. In the Medium and Long Term alternatives the marsh area available for sediment deposition and transport expands with increasing tidal wetland restoration at N. Deer Island Basin.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis DRAFT Final Report: June, 2016

Table 5‐1: Alternative Analysis Results – Q10 Short Term Delta Medium Term Delta Long Term Delta Novato Creek Existing Conditions (Change in Predicted Value) (Change in Predicted Value) (Change in Predicted Value) Max Max Max Max Max Max Total Max Max Total Max Max Total Max Max Total Flow Flow Flow Flow Location Roughness Slope Velocity Depth Volume Velocity Depth Volume Velocity Depth Volume Velocity Depth Volume Rate Rate Rate Rate (ft/sec) (ft) (AC‐FT) (ft/sec) (ft) (AC‐FT) (ft/sec) (ft) (AC‐FT) (ft/sec) (ft) (AC‐FT) (cfs) (cfs) (cfs) (cfs) DS Stafford 0.045 6.68% 319 5.0 2.6 721.2 0 0.0 0.0 0 ‐193 ‐1.5 ‐0.9 ‐441 ‐193 ‐1.5 ‐0.9 ‐441 Dam Sutro 0.045 0.33% 1306 3.4 8.9 1442.4 ‐37 0.0 ‐0.1 0 ‐163 ‐0.1 ‐0.5 ‐439 ‐140 ‐0.1 ‐0.5 ‐445 Simmons 0.045 0.56% 2162 3.1 13.7 2019.3 ‐43 0.0 ‐0.1 0 ‐233 ‐0.2 ‐0.5 ‐436 ‐208 ‐0.2 ‐0.5 ‐445 7th Street 0.045 0.68% 2111 4.2 12.1 2059.2 ‐25 0.0 ‐0.1 0 ‐182 ‐0.2 ‐0.3 ‐430 ‐219 ‐0.1 ‐0.4 ‐439 DS Diablo 0.045 0.10% 1966 6.1 13.7 2028.5 ‐5 0.0 0.0 6 ‐81 ‐0.1 ‐0.3 ‐411 ‐66 ‐0.1 ‐0.2 ‐417 (inflow) DS 101 0.045 0.06% 2702 1.5 13.4 3065.8 ‐122 0.3 ‐2.2 ‐114 ‐134 0.8 ‐3.2 ‐488 55 1.3 ‐4.1 ‐463 Warner Creek Existing Conditions Short Term Delta Medium Term Delta Long Term Delta McClay 0.045 0.16% 552 2.5 8.5 478.7 20 0.0 0.0 0.0 20 0.0 0.0 0.0 ‐7 0.0 ‐0.1 0.0 Tamalpais 0.045 0.33% 908 3.8 9.1 665.9 0 0.0 0.0 0.0 0 0.0 0.0 0.0 2 0.0 0.0 0.0 Warner US Novato Blvd 0.045 0.16% 800 1.7 11.1 865.4 24 0.1 ‐0.2 21.5 110 0.4 ‐0.2 21.5 ‐7 ‐0.2 ‐0.3 ‐76.7 (inflow) Arroyo Avichi Existing Conditions Short Term Delta Medium Term Delta Long Term Delta Arroyo Avichi to Novato 0.015 1.56% 202 6.7 4.8 279.9 ‐100 ‐3.3 0.0 ‐227.7 ‐138 ‐4.6 0.0 ‐243.1 ‐120 ‐4.0 0.0 ‐240.9 Creek Arroyo Avichi to Baccaglio 0.013 0.00% 210 2.9 8.4 54.3 145 2.3 ‐1.8 174.9 145 2.3 ‐2.4 175.8 145 3.9 ‐4.6 175.8 Basin Other Existing Conditions Short Term Delta Medium Term Delta Long Term Delta Grant Ave. Towards Rush Varies Varies 51 1.3 1.7 14.4 ‐15 0.0 ‐1.3 ‐3.9 ‐51 ‐1.3 ‐1.7 ‐14.4 ‐51 ‐1.3 ‐1.7 ‐14.4 Creek

Cross Valley Varies Varies 0 0.0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0.0 0.0 0 0.0 0.0 0.0 Flows

Center Road Varies Varies 14 0.7 1.7 28.5 0 0.0 ‐0.2 ‐2.9 ‐2 ‐0.1 ‐0.3 ‐3.9 ‐2 ‐0.7 ‐0.3 ‐4.4

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis DRAFT Final Report: June, 2016

Table 5‐2: Alternative Analysis Results – Q50 Short Term Delta Medium Term Delta Long Term Delta Novato Creek Existing Conditions (Change in Predicted Value) (Change in Predicted Value) (Change in Predicted Value) Max Max Max Max Max Max Total Max Max Total Max Max Total Max Max Total Flow Flow Flow Flow Location Roughness Slope Velocity Depth Volume Velocity Depth Volume Velocity Depth Volume Velocity Depth Volume Rate Rate Rate Rate (ft/sec) (ft) (AC‐FT) (ft/sec) (ft) (AC‐FT) (ft/sec) (ft) (AC‐FT) (ft/sec) (ft) (AC‐FT) (cfs) (cfs) (cfs) (cfs) DS Stafford Dam 0.045 6.68% 988 6.4 4.4 1104.8 0 0.1 0.0 0 ‐303 ‐0.6 ‐0.7 ‐473 ‐303 ‐0.6 ‐0.7 ‐473 Sutro 0.045 0.33% 2618 4.1 12.3 2712.9 6 0.0 0.0 ‐3 ‐260 ‐0.1 ‐0.6 ‐482 ‐328 ‐0.1 ‐0.8 ‐491 Simmons 0.045 0.56% 3259 4.6 15.9 3590.6 ‐11 0.0 0.0 0 166 ‐0.1 ‐0.1 ‐430 ‐90 ‐0.1 ‐0.2 ‐430 7th Street 0.045 0.68% 2344 4.4 12.7 3345.1 5 0.0 0.0 0 149 0.0 0.0 ‐362 ‐1 0.0 0.0 ‐356 DS Diablo (inflow) 0.045 0.10% 2046 6.2 14.0 3130.3 8 0.1 0.0 31 5 0.0 0.0 ‐313 5 0.1 ‐0.1 ‐310 DS 101 0.045 0.06% 4044 2.0 14.3 4787.5 582 1.1 ‐2.4 61 330 1.0 ‐2.6 ‐276 371 1.3 ‐3.1 ‐276 Warner Creek Existing Conditions Short Term Delta Medium Term Delta Long Term Delta McClay 0.045 0.16% 878 2.5 10.7 893.0 17 0.1 0.0 ‐3.1 328 0.1 ‐0.3 ‐12.3 ‐44 0.1 ‐0.4 ‐18.4 Tamalpais 0.045 0.33% 2016 4.3 12.8 1264.4 12 0.0 0.0 0.0 41 0.0 ‐0.3 ‐49.1 ‐243 0.0 ‐0.4 ‐36.8 Warner US Novato Blvd (inflow) 0.045 0.16% 1289 2.1 12.4 1335.0 89 0.1 ‐0.2 43.0 389 0.2 ‐0.3 21.5 58 0.1 ‐0.4 33.8 Arroyo Avichi Existing Conditions Short Term Delta Medium Term Delta Long Term Delta Arroyo Avichi to Novato Creek 0.015 1.56% 308 10.3 4.8 672.1 ‐32 ‐1.1 0.0 ‐374.1 ‐42 ‐1.4 0.0 ‐437.9 ‐44 ‐1.5 0.0 ‐517.1 Arroyo Avichi to Baccaglio Basin 0.013 0.00% 378 4.2 9.0 469.5 359 0.6 ‐0.2 30.7 358 0.7 ‐0.2 30.7 432 1.1 ‐0.4 30.7 Other Existing Conditions Short Term Delta Medium Term Delta Long Term Delta Grant Ave. Towards Rush Creek Varies Varies 367 3.2 1.3 37.3 ‐4 0.0 0.0 0.1 ‐14 ‐0.1 0.0 ‐5.3 ‐20 ‐0.2 0.0 ‐4.9

Cross Valley Flows Varies Varies 258 6.1 1.3 1.8 ‐6 ‐0.2 0.0 ‐0.6 ‐102 ‐1.3 ‐0.2 ‐0.8 ‐145 ‐1.8 ‐0.4 ‐1.0

Center Road Varies Varies 464 3.6 3.5 87.6 ‐26 ‐0.1 ‐0.1 ‐7.8 ‐54 ‐0.3 ‐0.2 ‐15.8 ‐203 ‐1.1 ‐0.6 ‐35.5

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis DRAFT Final Report: June, 2016

Table 5‐3: Alternative Analysis Results – Q50 Short Delta Medium Delta Long Delta Novato Creek Existing Conditions (Change in Predicted Value) (Change in Predicted Value) (Change in Predicted Value) Max Max Max Max Max Max Total Max Max Total Max Max Total Max Max Total Flow Flow Flow Flow Location Roughness Slope Velocity Depth Volume Velocity Depth Volume Velocity Depth Volume Velocity Depth Volume Rate Rate Rate Rate (ft/sec) (ft) (AC‐FT) (ft/sec) (ft) (AC‐FT) (ft/sec) (ft) (AC‐FT) (ft/sec) (ft) (AC‐FT) (cfs) (cfs) (cfs) (cfs) DS Stafford 0.045 6.68% 1377 7.0 5.1 1568.2 0 0.1 0.0 0 ‐308 ‐0.4 ‐0.6 ‐513 ‐308 ‐0.4 ‐0.6 ‐513 Dam Sutro 0.045 0.33% 3345 4.4 15.2 3652.0 ‐8 0.0 ‐0.1 0 ‐403 ‐0.2 ‐2.1 ‐552 ‐487 ‐0.2 ‐2.3 ‐552 Simmons 0.045 0.56% 3386 4.8 16.2 4511.3 ‐8 0.0 0.0 0 235 ‐0.1 ‐0.1 ‐430 ‐60 ‐0.1 ‐0.1 ‐430 7th Street 0.045 0.68% 2357 4.4 12.7 4050.9 2 0.0 0.0 31 152 0.0 0.0 ‐307 ‐3 0.0 0.0 ‐276 DS Diablo 0.045 0.10% 2049 6.2 14.1 3713.3 8 0.1 0.0 31 6 0.0 0.0 ‐215 8 0.0 ‐0.1 ‐215 (inflow) DS 101 0.045 0.06% 4454 2.2 14.4 5554.7 425 0.8 ‐1.8 307 311 1.0 ‐2.4 ‐31 246 1.3 ‐3.0 ‐31 Warner Creek Existing Conditions Short Term Delta Medium Term Delta Long Term Delta McClay 0.045 0.16% 1093 2.7 11.8 1236.8 92 0.2 0.1 ‐61.4 419 0.2 ‐0.3 ‐92.1 ‐48 0.1 ‐0.5 ‐110.5 Tamalpais 0.045 0.33% 2265 4.7 13.3 1678.7 14 0.0 0.0 33.8 ‐46 ‐0.1 ‐0.1 ‐58.3 ‐78 ‐0.1 ‐0.2 ‐52.2 Warner US Novato Blvd 0.045 0.16% 1397 2.2 12.7 1635.7 85 0.1 ‐0.1 119.7 64 0.1 ‐0.2 ‐24.6 53 0.1 ‐0.3 52.2 (inflow) Arroyo Avichi Existing Conditions Short Term Delta Medium Term Delta Long Term Delta Arroyo Avichi to Novato 0.015 1.56% 329 11.0 4.8 1166.2 ‐30 ‐1.0 0.0 ‐616.8 ‐40 ‐1.3 0.0 ‐742.7 ‐50 ‐1.7 0.0 ‐791.8 Creek Arroyo Avichi to Baccaglio 0.013 0.00% 463 5.1 9.0 399.0 415 0.2 ‐0.1 211.8 415 0.2 ‐0.1 211.8 415 0.2 ‐0.1 211.8 Basin Other Existing Conditions Short Term Delta Medium Term Delta Long Term Delta Grant Avenue Towards Rush Varies Varies 387 3.0 1.3 70.6 2 0.5 ‐0.1 ‐7.6 ‐4 0.4 ‐0.1 ‐20.5 ‐7 0.4 ‐0.1 ‐20.1 Creek

Cross Valley Varies Varies 711 8.1 2.0 6.1 ‐15 ‐0.3 0.1 ‐1.0 ‐197 ‐0.6 ‐0.3 ‐1.9 ‐286 ‐0.7 ‐0.4 ‐3.3 Flows

Center Road Varies Varies 637 4.5 3.9 137.2 ‐16 0.0 ‐0.1 ‐33.1 ‐46 ‐0.1 ‐0.1 ‐15.2 ‐141 ‐4.5 ‐0.3 ‐41.9

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis DRAFT Final Report: June, 2016

Table 5‐4: Predicted Peak WSEs for Novato Baylands WSE MAXIMUM (NAVD88‐ft) Q10 + 1‐ft SLR Diablo Ave. Nave Gardens NWPRR Mid DIB DS Hwy 37 BMKCSD No. Lock CABMK Breach Existing Conditions 15.74 13.67 13.38 12.17 10.85 9.03 7.80 Short Term 14.68 10.98 10.21 10.11 9.43 8.72 7.72 Medium Term 15.34 10.27 8.90 8.85 8.36 7.42 7.28 Long Term ‐‐‐‐‐‐‐ Q50 Existing Conditions 16.38 14.60 14.21 13.14 11.09 9.22 7.42 Short Term 15.34 12.49 11.39 11.22 10.42 9.55 7.68 Medium Term 15.85 11.93 10.44 10.32 9.45 7.57 6.78 Long Term 15.79 11.52 9.32 9.24 8.70 7.07 6.62 Q100 Existing Conditions 16.48 14.69 14.26 13.20 11.18 9.33 7.48 Short Term 15.47 12.74 11.59 11.42 10.47 9.63 7.71 Medium Term ‐‐‐‐‐‐‐ Long Term 15.86 11.69 9.82 9.71 9.09 7.24 6.73

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June 2016

Figure 5‐1: Q10 Existing Conditions Flood Depth (above) and Short Term Alternative Changes in Flood Plain Inundation (below) 5‐10

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June 2016

Figure 5‐2: Q50 Existing Conditions Flood Depth (above) and Short Term Alternative Changes in Flood Plain Inundation (below) 5‐11

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June 2016

Figure 5‐3: Q100 Existing Conditions Flood Depth (above) and Short Term Alternative Changes in Flood Plain Inundation (below) 5‐12

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June 2016

Predicted Water Surface Elevation Maxima for Design Storm Events 18 Legend EC Q10 + 1‐ft SLR EC Q50 EC Q100 16 Short Term Q10 + 1‐ft SLR Short Term Q50 Short Term Q100

14 (ft)

MCDNo. BMKCSD

12 Breach CABMK Elevation

WS

Lock

10 aeGardens Nave

8 Diablo SHWY DS i DIB Mid NWPRR

Ave.

37

6 40,000 35,000 30,000 25,000 20,000 15,000 10,000 5,000 0 Upstream Distance Upstream From San Pablo Bay (feet) Downstream

Figure 5‐4: Novato Bayland Changes in Short Term Peak Flood Water Surface Elevations

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis DRAFT

Figure 5‐5: Q10+1ft ‐ Existing and Short Term Alternative Water Surface Elevation at Max Flood 5‐14

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis DRAFT

Figure 5‐6: Q50 ‐ Existing and Short Term Alternative Water Surface Elevation at Max Flood 5‐15

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis DRAFT

Figure 5‐7: Q100 ‐ Existing and Short Term Alternative Water Surface Elevation at Max Flood 5‐16

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis DRAFT

Table 5‐5: Predicted Peak Flood Velocities for Novato Baylands VELOCITY AT FLOOD STAGE (ft/s) Q10 + 1‐ft SLR Diablo Ave. Nave Gardens NWPRR Mid DIB DS Hwy 37 BMKCSD No. Lock CABMK Breach Existing Conditions 7.45 2.57 1.81 1.80 2.05 2.09 1.80

Short Term 7.17 2.12 1.31 1.17 2.05 2.45 3.21 Medium Term 7.90 5.32 3.18 0.37 2.14 0.14 0.09 Long Term ‐‐‐‐‐‐‐ Q50 Existing Conditions 7.02 3.21 2.05 2.44 2.24 2.49 2.91 Short Term 8.23 4.95 3.21 1.88 3.09 2.76 3.29 Medium Term 7.63 5.70 3.67 0.44 3.20 1.50 1.41 Long Term 7.67 6.88 4.52 0.40 2.28 1.13 1.07

Q100 Existing Conditions 6.94 3.31 2.09 2.59 2.28 2.56 3.03 Short Term 8.10 5.03 3.27 1.81 3.00 2.77 3.51 Medium Term ‐‐‐‐‐‐‐ Long Term 7.64 6.49 4.21 0.39 2.68 1.39 0.60

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Predicted Water Surface Elevation Maxima for Design Storm Events 12 Legend EC Q10 + 1‐ft SLR EC Q50 EC Q100 10 Short Term Q10 + 1‐ft SLR Short Term Q50 Short Term Q100

8 MCDNo. BMKCSD AM Breach CABMK (ft/s) 6 Velocity

Lock

4 aeGardens Nave

2 Diablo SHWY DS NWPRR i DIB Mid

Ave. 37

0 35,000 30,000 25,000 20,000 15,000 10,000 5,000 0 Upstream Distance Upstream From San Pablo Bay (feet) Downstream Figure 5‐8: Novato Bayland Changes in Short Term Peak Flood Velocity

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Q50 EXISTING

Q50 SHORT

Figure 5‐9: Bed Shear Stress at Max Flood for Existing Conditions (above) and Short Term (Below) 5‐19

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Medium Term Alternative Analysis Summary Medium Term Alternative Elements, which include both Short and Medium Term Actions yield an increase in peak flood benefit both in Creek and Bayland reaches. Raising Stafford Dam and adding Bowman Canyon floodplain restoration results in a more marked decrease in peak flood water surface elevations between Sutro Ave and Diablo Ave. Medium Term actions in Novato baylands which expand of floodplain at Deer Island and East Basins, and channel cross section at Hwy 37 lower bayland flood peaks and reduce the volume of overbank flooding.

Figures 5.10 through 5.12 present the predicted existing conditions inundation depths, and the change in floodplain inundation depth associated with the Medium Term Alternative for Q10, Q50 and Q100 events. At Q10, the addition of Stafford Dam storage and Bowman Creek floodplain restoration yield small but measurable (0.3‐0.5 ft.) decreases in WSE along the Novato Creek corridor between Simmonds dLane an Diablo Ave. Figure 5.10 maps the associated floodplain benefits, which reduces the depth of flooding over a large portion of the inundated extent, and yields a 40% decrease in the number of buildings impacted on the floodplain. The greatest peak flood WSE reductions are predicted along Redwood Blvd. north of Diablo Ave./Delong Ave. as well as north and south of Novato Blvd. between Seventh St. and Diablo Ave.

Medium Term Alternative benefits in the Novato Creek corridor are significantly less at Q50/Q100 (Figure 5.12 and 5.13) where there is a small (5%) but area wide reduction in flood impact (Figure 5.14 and 5.15). Variation in flow structure is complicated by the change in cross basin flows at Q50. Medium term actions reduce the overbank flow volume downstream of Miwok Park by 34%. The reduction of these flows, which cross from Novato Creek to Warner Creek drainages shifts much of the peak flood WSEs reductions to the Vineyard/Warner Creek corridor. Water depth decreases of 0.3 ft predicted along Warner Creek in the Medium Term scenario. Reductions predicted along Novato Creek corridor were nominal (0‐0.1 ft.) at Simmonds Ln. The hydraulic model predicts that Medium term actions provide benefit to Warner creek by reducing Novato Creek flows to Warner. A greater volume of flood/floodplain storage will be required to mitigate both the cross valley flows and the flooding in the lower Novato Creek corridor. This trend occurs and is more pronounced in the Q100 results, where again there is no significant change in middle reaches of Novato Cr., while Warner Creek stage decreases 0.2 to 0.3 ft along the corridor. Maps illustrating the locations associated with changes in peak flood stage are included in Attachment D.

Adjacent to the confluence reach, in the tidally influenced portion of the creek, flood decreases may be attributed to the both upstream actions, and to reductions in peak flood WSE created by bayland actions which reduce Novato Creek and Warner Creek peak flood WSEs 0.2‐0.3 ft in the northern portion of the confluence reach, and two to four feet in the lower and upper baylands respectively. At Q10, the pump in Nave Gardens near Joan Ct. also provides a distinct local 1‐2 ft benefit to this low lying community (dark green on Figure 5.10).

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Table 5.4 and Figure 5.13 present the changes in bayland WSE maxima associated with Medium Term alternative actions. The Novato bayland model predicts Medium actions would decrease peak flood WSE up to 0.4 ft near Diablo Ave; with significantly greater reductions downstream. Flood crest reductions are predicted throughout the bayland due to both lower water surface elevations as the start of the storm events, and more rapid attenuation of flood hydrographs across the expanded tidal floodplain at No. Deer Island, West and East basins. The biggest flood crest reductions occur at Q10; with peak stage decrease 3.4 to 4.5 ft upstream of Hwy 37. Crest reductions decrease bayward from 2.5 ft. at the BMK No. Lock to 0.5 ft. at the proposed BMKV breach site4. The Medium Term water surface profiles are 1.1‐1.3 ft lower than the Short Term WSEs as a result of the added work. At Q50 flows5 channel expansion via sediment removal at Hwy 37 and the East Basin breach increase downstream conveyance through the bayland to provide a consistent drop in peak flood water levels through the corridor. As a result, Q50 Medium Term flood crests drop approximately 3.5 ft. and 1.5 ft. below the Existing Conditions WSE peaks at the SMART Bridge and BMK No. Lock respectively.

Medium term actions also results in less levee overtopping and unconstrained flooding in the corridor. Figure 5.14 indicates that Medium term actions effectively contain flooding within the corridor, while the triggering both the No. Deer Island Basin Spillway and the Pacheco Pond spillway to BMKV. As a result, Q10 flooding is abated at both Hwy 37 and Pacheco pond. At Q50 flows (Figure 5.15) peak flood WSEs decrease across both the upper and lower bayland reaches, and overbank flooding is abated throughout the corridor. In comparison to Short term actions, WSE reductions are continuous across Hwy 37 and increased by the restoration of East Basin tidal exchange. Lower bayland WSE reductions are greatest at and upstream of the breach at BMK South lock into the East Basin. The hydraulic model predicts that water surface elevation decreases attenuate with distance downstream along the main Novato Creek channel. Q100 flows were not evaluated for the Medium Term Alternative.

Predicted changes in peak flood velocities associated with the Medium Term Alternative are summarized in Table 5.5 and plotted in Figures 5.16. At Q10 and Q50 flows, the Medium Term Alternative increases bayward velocities 1.5 to 2 ft/sec from Diablo Ave. to No. Deer Island Basin. This indicates Medium Term actions in the upper bayland further increase bayward sediment transport capacity in the dredge reach. At Hwy 37, Q10/Q50 velocities are comparable through the crossing to those predicted for the Short Term Alternative. In the lower bayland (downstream of Hwy 37) channel velocities decrease with downstream distance. Q50 velocities are approximately 1.5 ft/sec higher than Q10 velocities through the reach. Predicted bed shear stress for the Medium Term alternative (Figure 5.17) indicate high shear values propagate further into No. Deer Island

4 Note: The Q10 and Q50 Medium term curves which would converge at San Pablo Bay cross downstream of BMK No. Lock because the Q10 results include 1ft. SLR. 5 Note: Q100 flows were not evaluated for the Medium Term alternative. 5‐21

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Basin than existing and short term scenarios. In the lower bayland, bed shear is high immediately downstream of Hwy 37, indicating scour is likely immediately downstream of the expanded sections. Post construction scour is also likely in Novato Creek channel between the restored West and East Basins.

Downstream of the BMK South Lock, high velocity/shear is conveyed into the East Basin breach, while the lowered levee alignments maintain flow within the Novato Creek channel. Shear reductions indicate significantly lower scour pressure along the old creek alignment near BMKs Montego Key park and downstream of the BMK So. Lock. Shear forces increase, and extend along the new East Basin breach alignment. These results suggest that proposed changes could support redirection of peak flood away from BMK levees and into/through West and East Basins. Final design should consider additional West Basin levee setbacks to along the Hwy 37 alignment, or shoreline protection measures for adjacent BMK properties. Similarly, tidal wetland restoration design for the East Basin should incorporate careful consideration of breach location, alignment and the distribution of flow between the existing channel and the subsided basin6.

6 Evaluation and design of interior basin hydraulics and circulation were not within the scope of this broader hydraulic study. 5‐22

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

a.

Figure 5‐10: Q10 Existing Conditions Flood Depth (above) and Medium Term Alternative Changes in Flood Plain Inundation (below) 5‐23

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐11: Q50 Existing Conditions Flood Depth (above) and Medium Term Alternative Changes in Flood Plain Inundation (below) 5‐24

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐12: Q100 Existing Conditions Flood Depth (above) and Medium Term Alternative Changes in Flood Plain Inundation (below) 5‐25

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Predicted Water Surface Elevation Maxima for Design Storm Events 18 Legend

EC Q10 + 1‐ft SLR

EC Q50 16 Short Term Q10 + 1‐ft SLR

Short Term Q50

Medium Term Q10 + 1‐ft SLR

14 Medium Term Q50 (ft)

MCDNo. BMKCSD AM Breach CABMK 12 Elevation

WS

Lock

10

8 Gardens Nave Diablo SHWY DS NWPRR i DIB Mid

Ave.

37

6 35,000 30,000 25,000 20,000 15,000 10,000 5,000 0 Upstream Distance Upstream From San Pablo Bay (feet) Downstream

Figure 5‐13: Novato Bayland Changes in Medium Term Peak Flood Water Surface Elevations

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Novato Creek Watershed Project: Alternatives Development and Hydraulic Analysis

Figure 5‐14: Q10 – Existing and Medium Term Alternative Water Surface Elevation at Max Flood 5‐27

Novato Creek Watershed Project: Alternatives Development and Hydraulic Analysis

Figure 5‐15: Existing and Medium Term Alternative Water Surface Elevation at Max Flood 5‐28

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐16: Novato Bayland Changes in Medium Term Peak Flood Channel Velocities

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐17: Bed Shear Stress at Max Flood for Existing Conditions (above) and Medium Term Alternative (below) 5‐30

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Long Term Alternative Analysis Long Term Alternative Elements include Short Medium and Long term actions. Two Creek elements are added to the Long Term Alternative. Floodplain restoration area is added upstream of Sutro Ave at Ohair Park, and in the Lower Warner Basin, storm drain capacity is increased to consolidate and drain accumulating flood waters along So. Novato Blvd. In the Baylands, Novato Creek north bank levees at No. Deer Island Basin and East Basin are set back to the bayland perimeter. The predicted peak flood WSEs and changes from existing conditions associated with the Long Term Alternative are summarized in Tables 5.1 through 5.4 and described below. Figures 5.18 through 5.20 present the predicted existing conditions inundation depths, and the change in floodplain inundation depth associated with the Long Term Alternative for Q10, Q50 and Q100 events.

At Q10, the addition of Ohair Park floodplain restoration led small but measurable 5(0.3 ‐0. ft.) decreases in WSE along the Novato Creek corridor between Simmonds Ln. and Diablo Ave.. Larger benefits (shown in darker shades of green) were achieved in the lower creek corridor and bayland due to the added conveyance to Lynwood Basin, and the expansion of bayland floodplain. The Long Term Alternative resulted in a predicted 40% decrease in the number of buildings impacted on the floodplain at Q10. The greatest peak flood WSE reductions occur where the predicted depth of flooding under existing conditions is the largest, north and south of Novato Blvd. between Seventh St. and Diablo Ave. and in the lower Warner Creek drainage. Benefits are also predicted along Redwood Blvd. north of Diablo Ave./Delong Ave. WSE reductions in this low lying area, likely result from both upstream (creek) and downstream (bayland) driven the decreases in overbank flow volume, and decrease the volume of discharge to the Rush Creek drainage. Long Term Alternative results at Q50/Q100 design flows. (Figure 5.19 and 5.20) indicate that flood depth reductions are smaller at higher flows, and reduce the number of flooded structures by only 8% and 6% respectively as reflected in the number of buildings impacted. In the middle creek corridor, between Sutro Ave. and Seventh St./Tamalpais Ave., channel WSE decreases remain small (0.4‐0.5 ft), but are sufficient to drive corresponding reductions along contiguous overland drainage corridors within the City. The indicated corridors reflect those locations where future floodway improvements or additional upstream improvements would have the greatest efficacy. Comparable or slightly larger changes in the creek reaches occur in the Lower Warner Creek drainage, and in the Railroad Ave corridor which drains to Rush Creek. The disconnected area of peak flood WSE reduction at Railroad Ave. is likely to be due to a reduction of upstream overland inflow volume which is not well reflected in the peak flood WSE metric. Immediately adjacent to Novato/Warner Creeks, flooded depths decrease in the 0.5‐1.0 ft range as a results of the combined influence of creek and bayland actions.

Table 5.4 and Figure 5.21 present the changes in bayland WSE maxima associated with Long Term alternative actions at Q50/Q100 discharges. Peak flood WSE reductions are predicted throughout the bayland due to both lower water surface elevations as the start of the storm events, and more rapid attenuation of flood hydrographs across the expanded tidal floodplain at No. Deer Island, 5‐31

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

West and East basins. The hydraulic models predict implementation of Long Term actions would decrease peak flood WSE up to 0.5 ft near Diablo Ave; with significantly greater reductions downstream. The biggest flood crest reductions occur in the upper bayland. Compared to existing conditions, Long Term actions generate a peak stage decreases of 3.0 to 4.9 ft. at Q50, and a comparable reduction of 3‐4.5 ft. at Q100 upstream of Hwy 37. In comparison to the Short Term Alternative, this represents an additional 1‐2 ft. of WSE reduction across the upper bayland.

Downstream of Hwy 37 the Long Term Q50/Q100 WSE profiles are comparable in slope to Existing and medium term profiles. At Q50, Long Term actions generate a 2.4 to 0.8 ft. reduction as compared to existing conditions values, which is an incremental reduction of 0.75 to 0.2 ft relative to medium term actions. At Q100 WSE peaks follow a comparable profile to existing conditions values, with reductions of 2.0 ft. between Hwy 37 and the BMK North Lock. Benefits diminish with distance downstream, with only a 0.75 ft. reduction predicted at the BMK breach site.

Lower bayland benefits of the Long Term actions are notable in that they reduce peak flood elevations below 10 feet, the current FEMA 100yr flood standard, throughout the baylands for both Q50 and Q100 events. Long Term actions Q100 peak flood WSE values are less than the Q50 values predicted for the Medium Term Alternative. As in prior alternatives, this results is due incremental WSE decreases due to the combined effect of a the rapid attenuation of the fluvial flood wave across the now unobstructed baylands, and a reduction in the starting WSE in the basin at the time of flood which increases with the volume of tidal exchange . As discussed in Section 5.3, this tidal amplitude benefit can be expected to wane as sea level rises, but would provide 1‐2 ft of SLR attenuation for the Novato Creek watershed.

Long Term actions effectively constrain flooding throughout the bayland for Q50 AND Q100 design flows throughout the two day design storm events. The No. DIB storm water basin is partially filled in these events, as peak flood WSE remain above the spillway crest for a relatively short duration. As in the Medium Term alternative, flows are conveyed across the Hwy 37/RR corridor without adverse impact to facilities. The large increase in tidal flood storage capacity further reduces the bayward WSE gradient at peak flood both in the upper bayland and adjacent to BMK. Flood impacts adjacent to Pacheco Pond, and discharges to the BMK restoration site decrease with added flood stage reductions. As in the Medium term actions, WSE reductions are continuous across Hwy 37 and increased by the restoration of East Basin tidal exchange. At Q50 (Figure 5.22) flood stage reductions are consistent from Hwy 37 to downstream of the BMK South lock. Bayward of the BMK South Lock flood reductions decrease with discharges at the eastern most breach in East Basin. As in the Medium Term alternative, the hydraulic model predicts that water surface elevation decreases attenuate with distance downstream along the main Novato Creek channel. Comparable changes occur At Q100 (Figure 5.23) flood benefits are comparable with the exception of the unmodified reach between West and East basins. This narrow channel section reduces bayward

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

conveyance upstream. The added flood volume exceeds reach conveyance capacity, resulting in a local decrease in WSE reduction (lighter blue coloration) upstream of the section.

Long term actions create an additional increase in flood velocities into the baylands which is indicated by the upward and downstream shift of the associated velocity profiles (Figure 5.24). With implementation of Long Term actions, peak flood velocities of 4‐5 ft/sec occur as far downstream as the SMART Bridge, indicating an increase in the capacity to transport coarser sands into No. Deer Island Basin. As in the Medium Term alternative, the added tidal exchange results in stronger bayward sediment transport gradients, and higher velocities throughout the reach. Velocity increases would further reduce anticipated dredge maintenance in the confluence reach, as a result of this increase sediment transport capacity.

Within the NoDIB basin, Long Term velocities drop off quickly, and are comparable to those predicted for Medium Term actions. Thus, the hydraulic model predicts that during flood events the restored subsided basins will be strongly depositional, and that sediment transport out of the baylands and Novato Creek channel geometry will be dictated by tidal exchange. Course sand and gravels which are conveyed in peak floods will accumulate within the basins in alluvial deltas. Sands and finer grained material can be mobilized by tidal currents, and will be subsequently reworked by tidal forces post flood. Course sediment will accumulate in the basins, and may require adaptive management/maintenance if bars form which adversely impact low flow conditions. Therefore, source control is recommended in Novato Creek reaches upstream of the baylands reduce coarse sediment loading, and management costs/impacts.

At the Hwy 37 crossing, Long Term velocities rise to values near those observed under existing conditions, indicating that coarse material conveyance beyond the upper bayland is unlikely during high tide events. Downstream of Hwy 37 predicted velocities decrease bayward converging with the predicted medium term rates. These velocities are determined largely by the San Pablo Bay confluence channel geometry, which is twice that assumed for the Short Term alternative. Actual velocities across this transition zone will vary with tidal prism, channel cross section and mudflat elevation. Natural geomorphic adjustment of the channel can be expected to drive increases in channel width and depth in accordance with upstream tidal prism.

The predicted bed shear stress associated with the Long Term alternative (Figure 5.25) clearly illustrates the shift in coarse sediment transport capacity to one of sediment delivery to No. Deer Island basin. Further downstream, an increase in shear occurs where there is a reduction in channel cross section which constrains outflow and increases velocity locally. Basin specific restoration designs should consider both the longitudinal distribution of velocity within the bayland, and the shear stress distribution and maxima within basin being designed. Analysis should consider both peak flood conditions, evaluated here, flood recession and low flow conditions which rework influent alluvial sediment and transport bay sources sediment into the bayland. 5‐33

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐18: Q10 Existing Conditions Flood Depth (above) and Long Term Alternative Changes in Flood Plain Inundation (below) 5‐34

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐19: Q50 Existing Conditions Flood Depth (above) and Long Term Alternative Changes in Flood Plain Inundation (below)

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐20: Q100 Existing Conditions Flood Depth (above) and Long Term Alternative Changes in Flood Plain Inundation (below) 5‐36

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐21: Novato Bayland Changes in Medium Term Peak Flood Water Surface Elevations

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Novato Creek Watershed Project: Alternatives Development and Hydraulic Analysis

Figure 5‐22: Q50 ‐ Existing and Long Term Alternative Water Surface Elevation at Max Flood 5‐38

Novato Creek Watershed Project: Alternatives Development and Hydraulic Analysis

Figure 5‐23: Q100 ‐ Existing and Long Term Alternative Water Surface Elevation at Max Flood 5‐39

Novato Creek Hydraulic Study Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Predicted Water Surface Elevation Maxima for Design Storm Events 9

EC Q50

8 EC Q100

Short Term Q50

Short Term Q100 7 Medium Term Q50

Long Term Q50

6 Long Term Q100

5 (ft/s)

4 Velocity

3

2

1

0 35,000 30,000 25,000 20,000 15,000 10,000 5,000 0 Distance Upstream From San Pablo Bay (feet)

Figure 5‐24: Novato Bayland Changes in Long Term Peak Flood Channel Velocities

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Novato Creek Hydraulic Study Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐25: Bed shear Stress at Max Flood for Existing Conditions (above) and Long Term Alternatives (below) 5‐41

Novato Creek Hydraulic Study Alternatives Development and Hydraulic Analysis Final Report: June, 2016 5.2 Comparison of Short Medium and Long Term Altenatives A comparison of the changes in predicted flooding by design flow provides additional information about watershed response to the Hydraulic Study alternatives. In the Novato Watershed creek corridors, the greatest benefits are observed at Q107 flows, with lesser benefit found at Q50/Q1008. Because Q100 flows have a comparable peak to that of Q50, hydraulic analysis focuses on Q10 and Q50 design storms. As noted earlier, each alternative creates an incremental reduction in flooding for the given design storm. The predicted flood footprint and depth of Existing Conditions (EC) Q10, Q50 and Q100 nfloodplai inundation, and the change in floodplain inundation depth associated with each alternative are presented in Figures 5.26 and 5.27. In the urbanized creek corridor, the Novato and Warner Creeks flow at or above capacity in all design storms. As a result, the benefits of an alternative are limited by the capacity to provide needed flood storage or an alternative conveyance. In stark contrast, the large amount of capacity available in the Novato Baylands provides significantly more opportunity for flood mitigation. East of Hwy 101, maximum flood WSEs decrease with distance downstream under both existing and proposed conditions. When compared to current conditions, all Alternatives reduce peak flood water surface elevations and the areal extent of flooding, and increase bayward flow and sediment transport gradients in reaches as far upstream as Diablo Ave.

At Q10 flows (valley flooding depths decrease in parcels adjacent to the bayland and along the Novato and Warner Creek corridors. Short term actions reduce the number of flooded of structures primarily between Diablo Ave. and Seventh St, along the Redwood Blvd. drainage corridor to Rush Creek and in the lower Warner Creek drainage (Nave Gardens). Water depths increase in Scottsdale Marsh and Lynwood Basin as a result of added upstream inflows. Medium Term actions, which add Stafford Dam and upper creek floodplain storage, create the largest increment of improvement along these corridors. Long term actions reduce the depth of water on the floodplain, but create no measurable change in the number of impacted structures.

The Alternatives create larger Q10 peak flood WSE reductions in the baylands (Figures 5.28, 5.29 and 5.30), where opportunity exists to remove levees and utilize adjacent diked basins for more significant floodplain expansion. The Short Term Alternative lowers peak flood WSEs by 2‐3 ft upstream of Pacheco Pond, and shifts the water surface gradient maxima from Hwy 37 to the dredge reach. Conveyance limits at Hwy 37 and added discharge from Pacheco Pond reduce the benefits of Short term bayland actions downstream of Hwy 37. Medium term actions which expand the Hwy 37 conveyance cross‐section, add a discharge to BMK at Pacheco Pond and open East Basin

7 Q10, Q50 and Q100 refer to design storms of increasing magnitude. The number references the probability of occurrence of a storm event of a given size in any given year. For example, a Q10 event, commonly referred to as a 10‐ year storm, has a one in ten probability or 10% chance of occurring in any given year. The 50‐year (Q50) and 100‐year (Q100) storms have a 2% and 1% probability of occurrence in any given year. 8 In general, Q50 and Q100 storms have a comparable peak flood WSE. Q100 storms have a greater duration and storm volume. 5‐42

Novato Creek Hydraulic Study Alternatives Development and Hydraulic Analysis Final Report: June, 2016 to tidal exchange result in an additional 1.0‐1.5 ft decrease in peak flood WSEs from the confluence reach to the BMK South Lock, as well as a reduction in the peak flood WSE at Pacheco pond.

At Q50 flows, creek discharges are well above available channel capacity, and there is significantly more water on the floodplain. The number of effected buildings increases from 419 at Q10, to 1215 at Q50. Implementation of the Short Term Alternative actions creates only nominal changes in flooded depth, and a 1% reduction in buildings impacted. (Many measures identified to increase benefit were removed from the scenario because implementation was deemed infeasible or they increased peaks flood WSEs downstream. Hydraulic models indicate that Medium and Long term Alternatives also have limited efficacy in lowering peak flood WSEs upstream of the baylands, and reducing the number of buildings impacted. Implementation of Medium and Long Term actions resulted in only a 5‐10% reduction in the number of building impacted. While there is benefit associated with proposed measures, these benefits generally increase drainage capacity, and improve the rate of flood recession but do not reduce the volume of depth of overbank flooding. Differences are difficult to discern when mapped as floodplain depths (Figure 5.31), but discernable when mapped as the change in depth across the floodplain (Figure 5.32).

While measures do not dramatically decrease flood peaks, increases in Lower Creek drainage will reduce the duration of flooding (i.e. the length of time for flooding) in the City. Increases in drainage and reductions in WSE were generated by all bayland actions, which reduce peak flood WSEs downstream of Diablo Ave. by approximately 0.5‐1 ft. at all evaluated discharges. Diablo Ave. is the approximately the limit of both current tidal influence and bayland actions benefit in the corridor.

The flood mitigation efficacy of the bayland Alternatives was sufficient to provide both peak flood WSE reduction benefits (Figure 5.28(b)) and a minimize overbank flooding in the corridor (Figure 5.29 and 5.30). At Q50, all three Bayland alternatives significantly decrease peak flood WSEs. The benefits of Short term actions occur in the upper baylands which most of the measures are implemented. Downstream of Pacheco pond, WSEs are largely unchanged by the added upstream conveyance. Medium and Long term actions each add a 1‐1.5 ft increments of WSE reduction across the bayland. These peak flood reductions reflect benefits associated with increasing floodplain expansion, and reduction in starting WSEs associated with the increasing bayland tidal prism. The progressive decrease in peak flood WSEs is indicated by the shifting color scales within the Novato Creek Channel and restored basins (Figure 5.33 and 5.34). These figures also show the decrease in the predicted locations of flooding in the corridor. At Q50, the Short Term alternatives limits flooding to the Hwy 37 crossing, and low lying parcels at BMK. Medium and Long term actions effectively constrain both Q50 and Q100 peak flows to the expanded Novato Creek corridor and engineered floodway locations including N. Deer Island Basin and the BMK restoration site. These conceptual designs indicate that flooding can be effectively managed within the bayland corridor utilizing measures which also reduce dredging and levee maintenance obligations. 5‐43

Novato Creek Hydraulic Study Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Velocities within the Novato baylands also change significantly with alternatives. In general, velocity structure becomes less uniform with each alternative. Novato Creek channel velocities into the baylands increases with water surface gradients as discussed above. Concurrently, channel velocities rapidly decrease where flows enter newly created tidal basins. The predicted change in velocity structure (Figure 5.35) results in an increase in sediment conveyance toward the newly restored tidal basins, and sediment deposition within the basins. The rate and location of sedimentation will depend on frequency, magnitude and recurrence of storm events. Appendix D presents the changes in velocity profiles in peak flood rfo bayland analysis scenarios.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐26: Valley Flood Inundation and Creek Depth Change at Q10: Existing/Short/Medium/Long (Clockwise Direction) 5‐45

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐27: Change in Valley Flood Inundation at Q10: Existing/Short/Medium/Long (Clockwise Direction) 5‐46

Novato Creek Hydraulic Study Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐28: Novato Baylands Water Surface Profile at Q10 (above) and Q50 (below) at Max Flood for Existing/Short/Medium/Long. 5‐47

Novato Creek Hydraulic Study: Alternatives Development andEXISTING Hydraulic Analysis SHORT Final Report: June, 2016

MEDIUM

Figure 5‐29: Q10 – Water Surface Elevation at Max Flood 5‐48

Novato Creek Hydraulic Study: Alternatives Development andEXISTING Hydraulic Analysis SHORT Final Report: June, 2016

MEDIUM

Figure 5‐30: Existing WSE and Changes at Max Flood: Short/Medium 5‐49

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐31: Valley Flood Inundation and Creek Depth Change at Q50: Existing/Short/Medium/Long (Clockwise Direction) 5‐50

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐32: Change in Valley Flood Inundation at Q50: Existing/Short/Medium/Long (Clockwise Direction) 5‐51

Novato Creek Hydraulic Study: Alternatives Development and HydraulicEXISTING Analysis SHORT Final Report: June, 2016

LONG MEDIUM

Figure 5‐33: Water Surface Elevation at Max Flood Existing/Short/Medium/Long (Clockwise Direction) 5‐52

Novato Creek Hydraulic Study: EXISTING SHORT Alternatives Development and Hydraulic Analysis Final Report: June, 2016

LONG MEDIUM

Figure 5‐34: Existing WSE and Changes at Max Flood: Existing/Short/Medium/Long (Clockwise Direction) 5‐53

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

12 12 Legend 10 Time:2.372 Pacheco Bottom Elevation

Redwood Velocity Magnitude: Base Case-Q50 9 Velocity Magnitude: Short Term Q50-ST Velocity Magnitude: Medium Q50-ST 8 Velocity Magnitude: Long Q50-ST 7 Rowland Ave Mid DIB Hwy37 Bridge RR Bridge 6 DS Hwy37 Tide Novato 4 CABMK Breach 4 BMKCSD No. Lock 2 Elevation (ft) Elevation Velocity (ft/s) Velocity 1 0 -1

-2 Warner Creek Arroyo Avichi -4 Nave Gardens -4 0 5000 10000 15000 20000 25000 30000 35000 Distance (ft)

Figure 5‐35: Longitudinal Profile of Flow Velocity at Max Flood

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016 5.3 Alternatives Analysis of Sea Level Rise Impacts Alternatives analysis considers SLR impacts by evaluating changes in flood hydraulics associated with design storms plus one foot and three feet of SLR at San Pablo Bay. As described in the Existing Conditions report (KHE, 2014), SLR was represented by simply adding a one or three foot increase to the spring tide boundary conditions. This preliminary conceptual analysis did not evaluate storm surge, which is not expected to exceed tidal WSEs assumed for the 3 ft SLR scenarios which raise San Pablo Bay tides to over 9.5 ft.

Seal level rise analysis provided the most positive findings in the corridor assessment. As expected, SLR impacts are greatest closest to San Pablo Bay where daily tidal fluctuations, peak flow and recession water levels fall within the range of the rising tides. Hydraulic modeling predicts that SLR driven tidal WSE increases will propagate upstream from San Pablo Bay to the confluence reach (Nave Gardens) with minimal high tide attenuation. However, one to three feet of sea level rise did not impact peak flood water surface elevations in reaches of Novato/Warner Creeks upstream of Hwy 37 (Figure 5.36). This result is due to the fact that peak flood WSEs are higher than tidal influence (approximately 10 ft NAVD88) under all scenarios As a result, creek modeling upstream of Diablo Ave which evaluated the change in flood peaks did not differ significantly from comparable runs without the elevated tidal boundary conditions.

While peak flood WSEs are not effected upstream of Hwy 37, Bayland modeling analysis indicates that more than 1 ft of SLR will reduce creek flood recession rates and bayward sediment transport gradients. SLR progressively increases the base level within the Novato Creek corridor from San Pablo Bay to Seventh Street, which is the current limit of tidal influence (the head of tide). This increase in base level reduces the effected slope of the creek, and will increase sedimentation rates throughout the corridor. Impacts increase with downstream distance as the daily tide range rises and intersects the flood recession curve with increasing frequency. With 3 ft of SLR, peak flood increases of 0.5 ft are predicted at Q50 at BMK No. Lock, and flood recession slows to zero as the daily tidal maxima approaches and exceeds the predicted Q50 peak flood values in the lower baylands. The benefits of Short, Medium and Long Term Alternative actions which reduce peak flood WSEs upstream of Pacheco Pond (above approximately 10 ft NAVD88) are retained for both the 1 ft sand 3 ft SLR scenarios (Figure 5.38). Unfortunately, downstream of Hwy 37, flood reductions gained through Alternative actions are lost to rising tides. Figure 3.39 illustrates the change in flooded WSE and area associated 3 ft SLR. Under existing conditions, the model predicts levee overtopping at Q50 throughout the lower Novato baylands, and while short and long term actions reduce flood peaks and flooding at Hwy 37, they are not sufficient to preclude levee at BMK and throughout the lower Novato baylands.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016 5.4 Alternative Analysis of Mid‐Tide Scenarios In an effort to characterize the change in predicted results when storm peaks occur during a more favorable tidal stage, simulations were also conducted using “mid‐tide” boundary condition scenarios. These flood simulations assume the peak discharge occurs at a mid‐tide (typically 3.4 ft NAVD88) during ebb flow conditions (i.e. when tidal stage is falling). Throughout the baylands, predicted changes in peak flood WSEs associated with mid‐tide conditions were generally comparable to those of the study baseline which assumes the peak of storm is coincident with high tide (Figure 5.41). The most notable difference in results occurs in the lower baylands, where the assumption of mid‐tide conditions increases flood recession rates and results is a slight (<0.25 ft reduction in the lower limit of predicted tide range. This comparison suggests that the timing of the tide not as significant an influence of the flood maxima as the starting water surface elevation in the restored tidal basins. Because the large restored tidal basins require multiple days to fill and drain, spring neap periods may be a more valuable indicator the potential range of flood water levels across the baylands. The mid‐tide scenarios also resulted in a slight (<‐.5 ft/s) upward shift in flood velocities in the lower bayland, due to the lower San Pablo Bay WSE during peak flood (Attachment E).

Figure 5‐36: Q50 – Existing WSE Changes with 1ft and 3ft Sea Leve Rise

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐37: Time Series at Q50 of Existing and Short Term Alternatives WSE Times Series at Nave Gardens, Mid DIB and BMK North Lock: Existing Conditions, 1ft SLR and 3 ft SLR 5‐57

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐38: Q50 – Existing and Short Term Alternative WSE Profile at Max Flood with 1ft Sea Level Rise (above) and 3 ft Sea Level Rise (below)

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Novato Creek Watershed Project: Alternatives Development and Hydraulic Analysis

Figure 5‐39: Q50 – Existing and Short/Medium/Long Alternatives Bayland WSEs at Max Flood with 3 ft Sea Level Rise 5‐59

Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

Figure 5‐40: Time Series at Q50 of Existing and Short Term Alternatives WSE Time Series at Nave Gardens, Mid DIB and BMK North Lock. Mid Tide Analysis

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

6 Study Conclusions 6.1 General Findings: Presented below are general findings for the Alternatives Analysis. These findings present both the improved understanding of watershed conditions, and the analysis of study alternatives.

1. The 1984 Novato Flood Control Project maximized conveyance through the Novato Creek study area. Despite these actions, Novato and Warner Creek are both near conveyance capacity at Q10 or greater discharges. . Ongoing flood plain development has further reduced capacity on the valley floor where creeks are undersized . Existing bridges pass flood waters and are not point sources of flooding . Channel area decreases downstream as discharge accumulates and generates overbank flooding . Conveyance oin Novat and Warner Creeks downstream of Seventh St. is reduced during high tide events.

2. In Q10 storm events:  Flooding occurs on Novato/Warner Creeks within the City limits and in the Novato Baylands.  Novato Creek overtops its banks and produces flooding upstream of Simmons Ln. where storm drains are undersized, and downstream of Seventh St. where accumulating inflows exceed channel capacity. Flooding along Novato Creek extends north toward Railroad Ave. which discharges to Rush Creek, and South toward Warner Creek. Flooding at both these locations results from both local high water in the creeks and the accumulation of floodwater from upstream watershed areas. . The valley floor dips south, conveying much of Novato Creek overbank flows upstream of Grant Ave. toward Warner Creek. . Warner Creek floods parcels to the North downstream of Seventh St. and to the south downstream of Diablo Ave. along both Center Rd. downstream of McClay Rd. and S. Novato Blvd. . Novato baylands flooding occurs first at the narrowed Hwy 37 crossing, slightly later in the storm period flooding overtops north and south levees at Pacheco Pond.

3. In larger storm events:  Flooding is concurrent on Novato and Warner Creeks, and theree ar no alternate routes with capacity  Flooding at the Miwok Park to Pioneer Park narrows acts to reduce flood pressure downstream on Novato Creek

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

 Overbank water flows west/south from Novato Cr. to Warner Cr. and beyond, and increases flooding in Warner Creek drainages  City storm drains exceed capacity and/or backwater creating localized flooding: upstream of Miwok Park; in the Rush Creek corridor: and in the lower Warner Creek drainage downstream of Seventh St. along Center Rd and S. Novato Blvd (Nave Gardens))

4. In a Q50 storm event: Creek flooding extends over much of the Novato valley along both Warner and Novato Creeks. Flood depths are typically less than one foot. Flooded depths of 1‐3 feet occur:  Adjacent to Vineyard Creek between Wilson Ave. and McClay Rd.;  Along Warner Creek from Grant Ave.to So. Novato Blvd;  Along Novato Blvd. upstream of Grant Ave.  Southeast of Diablo Ave. where high tides restrict drainage and accumulated water spreads north along Railroad Ave. and south along So. Novato Blvd. /Center Rd. . Downstream of Seventh St, Novato Creek flooding and backwater from adjacent storm drains pond to the north along Railroad Ave., and then flows north toward Rush Creek. Storm drain and creek outfalls along the Rush Creek drainage also do not have adequate storm capacity, and results in flooding to the hnort within the Rush Creek drainage. . Bayland flooding expands along the Hwy 37 corridor and at Pacheco Pond, inundating adjacent parcels. In addition, levees are overtopped adjacent Hwy 101, along the BMK Community North Lagoon, and at Lynwood and North Deer Island Basins. . High water levels are sustained in throughout Novato Creek for more than 5 days following the storm event, reducing drainage capacity from storm drains and outfalls.

5. In a Q100 storm event:  Peak flood discharges are comparable to Q50 flood maxima, because Novato’s creeks overtop their banks at the same elevations. The duration and volume of the Q100 storm are greater than that at Q50  The pattern of flooding is comparable to that at Q50 ‐ added volume results in deeper and more contiguous flooded areas encompassing much of Novato between Center Road and Grant Ave.  The greatest increase in creek flooding occurs along the Warner Creek corridor which receives both upstream inflows and overbank Novato Creek water. Novato Cr. flows south across Novato Blvd. and into the Warner Creek drainage both upstream of McClay Rd. and downstream of Seventh St. /Tamalpais Ave.  Bayland flooding expands cutting off access to critical facilities, inundating NSD treatment facilities, obstructing Hwy 37 and inundating buildings around Pacheco Pond and at BMK.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

6. Peak Flood Water Surface Elevations (WSEs):  Are comparable for Q50 and Q100 storm events because overbank flooding limits the maximum creek stage.  Rise at comparable rates in both Novato and Warner Creeks  Decrease with distance downstream from Stafford Dam to San Pablo Bay  Decrease rapidly within the confluence reach where the valley floor transitions to bayland creating a strongly depositional environment.  Increase locally and creates flooding at the Hwy 37/Railroad crossing due to narrowed levee alignments and an aggraded channel  Decrease rapidly with floodplain expansion and support natural deposition in Novato’s subsided bayland basins

7. Sea Level Rise  Can be expected to increase bayland water surface elevations 1‐3 feet creating daily high tides of 6‐9 ft within the 50‐year design horizon of this study.  Will increase daily tide maxima to 8‐10 ft. o Downstream of Hwy 37, this increases both daily tide range and peak flood water surface elevation (WSEs). The daily tidal maxima will increase to near or above current Q50 flood maxima, and results in less than 2‐3 ft of levee freeboard on most bayland levees o Upstream of the Hwy 37 this increase does NOT increase peak flood WSEs because flood stages rise above tidal influence to 10‐16 ft.  Reduces City outflow capacity and increases sedimentation in the already aggrading Novato/Warner Cr. confluence reach between Diablo Ave. and Rowland Ave.  Decreases bayland velocity maxima and slows flood recession in Novato/Warner Cr and across the baylands  Is expected to continue, reaching 4.5 ft. by 2100 (BCDC, 2014), propagating impacts upstream, and requiring increasing dependence on storm water storage during high tides.

8. Levee Setbacks (Relocation of Bayland Levees to widen the creek corridors):  Reduce peak flood WSEs by expanding the available conveyance area. These reductions will diminish over time due to sea level rise  Increase the rate of flood attenuation and recession  Increase bayward flow and sediment transport capacity during favorable tides  Increase tidal prism (the volume of water exchanged daily by the tide) and in turn the size of the channel that is maintained without dredging during low flow conditions.  Provide capacity for natural sedimentation and climate adaption

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

 Improve the extent and ecological values of tidal wetlands and the Novato/Warner Creek corridors

9. Tributary Floodplain Restoration:  Benefits are limited during if design storm events because elements do not retain a sufficient volume to provide downstream benefit  At lower flow regimes, elements would attenuate flooding, support ground water recharge in the riparian corridor ecotone, and reduces sediment loading to the creek  Would require expansion of floodplain or addition of main stem floodplain elements to increase floodplain storage, reduce downstream flow velocities and bed/bank erosion.

10. Drainage Improvements in Lower Warner Creek Basin  Increase the storm drainage volume by 30‐50%, with adequate downstream storage.  Significantly increase flood conveyance capacity and are not limited at high tide  Do not decrease peak flood WSEs locally because of the added upstream inflows  Increase the rate of overbank flood recession following large storm events  Warrant further consideration despite the limited reduction in peak flood water surface maxima

6.2 Alternative Analysis Conclusions Short, Medium and Long Term Alternatives provide an incremental reduction on overbank flooding with each Alternative. Conclusion and recommendations for each alternative are presented below.

Short Term Alternative Elements: . Incrementally decrease but do not eliminate creek and bayland flooding . Have the greatest benefit in Novato Creeks upstream of tidal influence at Q10, and limited benefit upstream of tidal influence at Q50 and Q100 when the creek flows significantly exceed capacity. Short term benefits within the Novato Baylands are significantly greater yield peak flood WSE reductions of 1‐3 feet in the confluence reach and northern portion of the Upper Baylands for all design storm scenarios. . Increase flood recession rates and accelerate drainage from low lying areas . Increase flood conveyance capacity on Warner Creek during high tides by routing water downstream via Scottsdale Marsh and Lynwood Basin . Reduce bayland WSE maxima (1‐3+ ft.) and the location and volume of flooding . Limit Q10 bayland flooding to areas around Hwy 37 . Increase dredging efficiency without increased flooding . Add valuable estuarine habit

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

. Yield benefits primarily upstream of Hwy 37 due to limited conveyance at Hwy 37, and reducing the efficacy of West Basin tidal floodplain restoration . Support sea level rise adaption by reducing daily tide range

Medium Term Elements:  Significantly, reduces flooding across the watershed when compared to short term elements  Add dam storage (700 ac‐ft) and floodplain restoration in upstream reaches of Novato Creek provide significant reduction in the downstream flood volumes, allowing Novato Creeks to contain and convey a larger percentage of overbank waters.  Incrementally reduce bayland peak flood WSEs by attenuating peak flood volumes and lowering the daily tide range, and in turn, pre‐storm starting water levels across the bayland  Increase drainage capacity and sediment conveyance rates from low lying creek and watershed areas  In Novato baylands, contain and convey the 50 year storm events without overbank flooding  Removes a critical conveyance constriction at Hwy 37, increasing flow and sediment conveyance throughout the baylands  Incorporate expansive East Basin levee and infrastructure setbacks in the lower Novato baylands which lower flood peaks downstream of Hwy 37, increasing conveyance throughout the bayland and downstream by expanding channel geometry at the Novato Creek/San Pablo Bay confluence.

Long Term Elements:  Expand the work of medium term actions  Improve flood conveyance and reduce flooding in both the Creek and Bayland corridors.  Work to reduce the impacts (extent and duration) of flooding in City streets by expanding undersized storm drains and establishing corridors which constrain and convey overbank flows.  Reduce peak flood WSE an addition 2 ft across the baylands  Removes upland fill for beneficial reuse within the watershed  Reduces the opportunity for future expansion of storm water storage capacity in North Deer Island basin. Additional consideration of the future needs for storm water storage is warranted prior to conversion of all of Deer Island Basin to tidal wetland.

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

6.3 Recommendtaions

Recommendations for Next Phases of Work  Upper bayland short term elements which BOTH maximize downstream flow and sediment conveyance and increase downstream sediment storage capacity  Lower Warner drainage improvements to increase conveyance from So. Novato/Center Rd via Scottsdale Pond. Efforts should first address upstream conveyance improvements before increasing Arroyo Avichi diversions.  Beneficial reuse of dredged creek sediments. This coarse sediment is a valuable resource and should retained and utilized for anticipated levee improvements and/or realignment  Further evaluation of Medium Term elements which provided significant benefits and thereby may warrant reconsideration as short term actions: o Raise Stafford Dam and/or add storage upstream to reduce flood volumes o Expansion of Novato Creek at Hwy 37 to improve overall bayland flood and sediment conveyance

Additional Project Elements: The following additional elements project are recommended for considered as part of short term work and funding requests  Pacheco Pond water quality improvements. Poor water quality has been noted during prior summer low flow conditions which has created an odor nuisance for local residents, and may adversely impact ecological values in the brackish pond complex. Elements to evaluate pond sediment sources and improve circulation should be considered.  Coarse sediment management along Novato and Warner Creeks. Actions could include: o sediment removal from accessible aggrading bars o grade control structures to limit Warner Creek incision o Arroyo Avichi sediment removal upstream of the diversion to reduce confluence reach sedimentation locally and upstream o localized riparian floodplain restoration to reduce vegetation encroachment support channel storage

Concepts Recommended for Additional Study: The follow concepts warrant additional study to reduce flood risks and impacts, improve sediment management and ecological conditions in the watershed:  Evaluate Novato Creek main stem floodplain restoration o Increase flood storage and reduce peak flood flows o Reduce peak flow velocities and downstream scour and sediment transport o Increase ground water recharge and ecological conditions in the riparian corridor

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Novato Creek Hydraulic Study: Alternatives Development and Hydraulic Analysis Final Report: June, 2016

o Integrate this effort with raising Stafford Dam to maximize flood storage and peak flood attenuation upstream of the urban corridor

 Evaluate surface street/storm drain/sanitary line improvements along “floodways” to o reduce the impacts of extreme floods on property and infrastructure o increase flood recession rates and lessen the duration of storm impact o maintain access to critical facilities during storm events

 Evaluate additional options to increase flood storage and/or flow diversion upstream of Simmonds La. Including: o Storage above Stafford Dam o Novato Creek floodplain expansion upstream of Sutro Ave o Diversion of San Marin area drainages to Rush Creek Marsh o Local detention storage for tributary drainage areas

 Evaluate costs and impacts of realignment of lower bayland levees parallel to Hwy 37, to reduce the total length of levee required. This entails loss of NSD summer irrigation disposal capacity in both East and West Basins, and may alter flow patterns and navigable access in Novato Creek downstream of Hwy 37. This assessment should support efforts to secure cost share between MDPW and State/Federal transportation agencies who rely on MDPW infrastructure for coastal flood protection. The levees cost share should be evaluated based on all possible levee alignments, including the shortest possible alignment which is a cross levee from Deer Island to Lynwood Basin.

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