Completed draft for review 1 Summary of existing information in the Watershed of Sonoma Valley in relation to the Sonoma Creek Watershed Restoration Study and Recommendations on How to Proceed Prepared for the U.S. Army Corps of Engineers, San Francisco District by the San Francisco Estuary Institute and Sonoma Ecology Center V.2 December 2000 Completed draft for review 2 Bibliographic information This report should be referenced in the following manner: McKee, L., Grossinger, R., Brewster, E., Dale, R., Cornwall, C., Hunter, R., and Lawton, R. 2000. Summary of existing information in the watershed of Sonoma Valley in relation to the Sonoma Creek Watershed Restoration Study and recommendations on how to proceed. A report prepared by San Francisco Estuary Institute (SFEI) and Sonoma Ecology Center (SEC) for U.S. Army Corps of Engineers, San Francisco District. San Francisco Estuary Institute, December 2000. Completed draft for review 3 Table of contents Page Section 1 7 Summary, Scope, and historical timeline Executive Summary 8 Introduction and acknowledgements 16 Objectives for this document 18 A brief history of Sonoma Creek - relationships of people to the landscape 19 Section 2 25 Sonoma Creek Watershed Characteristics Introduction 26 Geology 26 Soils 28 Topography 29 Upper watershed 29 Marshlands 29 Watershed vegetation and land-use 31 Middle and upper watershed 31 Historical 31 Contemporary 31 Baylands 34 Historical 34 Contemporary 35 Riparian vegetation 36 Invasive Species 36 Middle and upper watershed 36 Baylands 37 Section 3 38 Weather, Climate, and Runoff General description 39 Rainfall 39 Rainfall records 39 Drought years and wet years 41 Monthly Rainfall variation 43 Frequency, depth and magnitude 43 Surface discharge 48 General description of data 48 Annual discharge 51 Normalized discharge and runoff coefficients 51 Dry season runoff 55 Watershed response to storm rainfall 57 Return period of floods 62 Flooding and inundation 64 Discussion of freshwater runoff issues 65 Definition of the flooding problem 65 Rainfall and runoff 66 Water delivery, collection, and treatment systems 71 Groundwater 71 Completed draft for review 4 Section 4 73 Tide gauge location, height, and tide induced flow Introduction 74 Location of Gauges 74 Tidal velocity measurements 75 Section 5 79 Water quality and sediment quality Water quality 80 Watershed 80 North San Pablo Bay and the Sonoma tidal channels 83 Sediment quality in the Sonoma Baylands 86 Section 6 87 Watershed and Baylands Fauna In-stream freshwater biota 88 Historical 88 Contemporary 88 Freshwater fisheries habitat and spawning sites 91 Estuarine biota spatial extent 92 Bird life, temporal and spatial extent 93 Historical 93 Contemporary 93 Section 7 95 Causes of flooding Introduction 96 Hypotheses 96 Section 8 99 Restoration projects: Historical and contemporary Review of the history of mitigation options 100 Sonoma Ecology Center restoration projects 102 Introduction 102 Past and current SEC Projects 102 Future SEC Projects 105 Options or issues in relation to habitat restoration in the lower Sonoma Creek watershed 110 Section 9 115 Guiding Principles for successful flood control and restoration Strong community involvement 116 Historical Landscape Ecology 118 What was the character of the historic system and how did we got to where we are today? 118 Integrated watershed approach 122 Integrated Bayland approach 123 Benefit to Habitats and Species of the Watershed 124 Preserving locations of importance 125 Completed draft for review 5 Section 10 126 Limitations of existing data Hydrology 127 Geomorphology and Water Quality 129 Biology 131 Riparian Conditions 131 Sensitive Species and Habitats 132 Steelhead and California freshwater shrimp 133 Benthic macro-invertebrates 133 Section 11 134 Recommendations for projects and estimated costs Introduction 135 Projects and Costs 137 Section 12 140 References Section 13 149 Appendices Appendix 1. Potential historical resources 150 Appendix 2. SFEI existing historical document list 155 Appendix 3. GIS coverage’s held by SEC 163 Completed draft for review 6 List of figure and tables Figures Page Figure 1. Sonoma Creek watershed including the Baylands 27 Figure 2. Sub-watershed boundaries in the Sonoma Creek watershed 30 Figure 3. Sonoma Creek watershed land use designations 33 Figure 4. Rainfall recorded for the City of Sonoma 40 Figure 5. Accumulative deviation from the mean calculated for rainfall in Sonoma 42 Figure 6. Monthly variation in rainfall for selected location in the North Bay 44 Figure 7. Relationship between rainfall falling at Sonoma and Petaluma Fire Station 45 Figure 8. Relationship between rainfall at Sonoma and rainfall at Napa 46 Figure 9. Duration and magnitude of rainfall for a given return period in the City of Sonoma 47 Figure 10. Sonoma Ecology Center Water Quality & Quantity Monitoring Sites 49 Figure 11. Daily runoff on Sonoma Creek at the discontinued runoff measuring point at Agua Caliente 52 Figure 12. Annual area normalized runoff variation for the period of record at Agua Caliente 53 Figure 13. Annual runoff coefficients for Sonoma Creek at Agua Caliente 54 Figure 14. An analysis of dry season flow at Agua Caliente 56 Figure 15. January 1967 storm in Sonoma Creek watershed 58 Figure 16. December 1955 storm in Sonoma Creek watershed 60 Figure 17. December 1965 / January 1966 storm in Sonoma Creek watershed 61 Figure 18. Return interval of floods in the North Bay watersheds for a selection of gauging stations 63 Figure 19. The effect of urbanization on peak runoff 68 Figure 20. A simple analysis of flood peaks based on the annual series for the Napa River near Napa 69 Figure 21. A simple analysis of flood peaks based on the annual series for the Napa River near Saint Helena. 70 Figure 22. A conceptual diagram for information gathering and determining option for the future 136 Tables Table 1. A timeline of events pertaining to the human relationship to the Sonoma Creek watershed 21 environment Table 2. Discharge characteristics of the Sonoma Creek watershed as determined in the 1960’s 52 Table 3. Historic data from Anon. (late 1950’s) describing runoff character in Sonoma Creek watershed 59 Table 4. Water quality collection points of Sonoma Valley County Sanitation District - NPDES Self- 83 Monitoring Program Table 5. The occurrence of fish species in freshwater areas of Sonoma Creek watershed 90 Table 6. Occurrence of fish in tidal areas of the Sonoma Creek watershed 92 Table 7. A history of the options and recommendations for dealing with flooding issues in the lower 100 Sonoma Creek watershed Table 8. Description of the importance of historical analysis in ecosystem process research, watershed 121 management plan design, and implementation of restoration projects Completed draft for review 7 Section 1 Summary, Scope, and historical timeline Completed draft for review 8 Executive Summary This report illustrates the variety of data available in relation to the future possibility of carrying out projects that aim to reduce flood hazard and restore or enhance environmental values in the Sonoma Creek watershed and Baylands. This report is meant to be a starting point for information and recommendations rather than an endpoint. Although it contains over 150 pages of text, figures and tables it does not claim to be complete. Instead it aims to stimulate discussion by asking as many questions as it answers. This report is one of two documents. The second document is the verbatim minutes of the technical advisory committee meeting held at Atwood Ranch on August 30th 2000. Both documents are available from San Francisco Estuary Institute (SFEI) or from the SFEI web page (www.sfei.org) in pdf format. There are five strong principles that have been reinforced during this review of information and during the technical advisory meeting: 1. That there be a strong community involvement, and this should drive the process of identifying potential actions. Community involvement includes: o Gathering and recording community opinions on what, if anything, should be done. o Community representation from all over the watershed and this should be encouraged at all stages, because the solutions are likely to involve the whole watershed community. o Gathering and recording both historical and contemporary environmental knowledge. o Consultation throughout the science and decision making phases. o Education about why any scientific, engineering or management alternatives are proposed so that the community is able to help make choices. 2. That the approaches to flood mitigation and environmental restoration consider the watershed as a whole. No single project will be able to achieve any substantial reduction in peak flow, total flood event discharge or flood routing. Instead, many small projects taking a variety of approaches across the whole watershed and Baylands would be more Completed draft for review 9 likely to provide ecosystem benefits, as well as achieving a reduction, or at least no increases, in flood risk in a bottom-up / top-of-the-watershed down approach. 3. That any Baylands projects consider the Napa / Sonoma Marsh as a whole. The Napa Sonoma Marsh system in linked closely both in space and time. Any changes in one “side” of the system are likely to affect the other “side” (physically, chemically and biologically). 4. That many options for reductions in flooding in the lower watershed are also consistent with the preservation or improvement of habitat, species numbers, and species diversity in the whole watershed. For example, planting and managing riparian vegetation to improve riparian connectivity and structure will reduce flooding in the lower watershed by slowing down the flood wave and increasing groundwater recharge. It will also improve habitat quality for fish, birds and invertebrates by decreasing water temperature, increasing in-stream habitat diversity, increasing carbon supply to the streams, and decreasing bank erosion. This intern will improve the environment for the people that live in and visit the watershed by providing a tranquil intact connection to the environment that can be enjoyed now and by future generations.