Introduction Upper Penitencia Creek has a history of flooding, particularly in its downstream reaches near the confluence with Coyote Creek. Because of this, the Santa Clara Valley Water District (District) recently initiated the Upper Penitencia Creek Project, with main goals including the prevention of flooding damage along the creek and shutdowns to utility and transportation infrastructure. The District is seeking a management approach for the creek that meets these goals in a manner that is resilient to changing land use and climatic conditions, while providing additional benefits beyond flood risk management, including maximizing water supply, supporting ecological processes and functions, and creating recreational opportunities. The District is also seeking to develop this new management approach in coordination with local partners who own and operate land adjacent to the creek (e.g., City of San Jose, County of Santa Clara, and local school districts), thereby explicitly incorporating the partners’ management goals into the approach and expanding the areas adjacent to the creek that could be managed to provide multiple benefits.

Though bound by a highly urbanized landscape in its lower reaches, Upper Penitencia Creek remains an important resource that provides ecological services that are relatively unique in Santa Clara Valley. For example, the creek provides vital habitat for threatened steelhead trout (Oncorhynchus mykiss) and other native fish species. In addition, public open spaces and forested natural areas along the creek corridor provide important habitat for native plants, amphibians, fishes, birds, and other wildlife, providing a major portion of what could eventually be a regionally important corridor of habitat connectivity from the Diablo Range in the eastern portion of Santa Clara Valley to the Bay.

Upper Penitencia Creek from the confluence with Coyote Creek upstream to Alum Rock Park.

1 As a first step in developing a new management approach for Upper Penitencia Creek that benefits both people and wildlife, the District, in partnership with the San Francisco Estuary Institute-Aquatic Science Center (SFEI-ASC), convened a workshop on March 13, 2017 aimed at creating a high level, science-based “landscape concept” for the area. The workshop included presentations by District engineers and planners and SFEI-ASC scientists on the historical and contemporary characteristics of

Upper Penitencia Creek and its surrounding Photo: Amy Richey landscape, including terrestrial and aquatic ecology, Creek field visit with the Science Hub members dry season and flood hydrology/hydraulics, and District staff (November 29, 2016). groundwater dynamics, and geomorphology. Information about current recreational and educational opportunities was also included. The presentations were followed by a moderated discussion that focused on the short- and long-term management measures put forth by an expert panel of science advisors, or Science Hub. The Hub members were Andy Collison (fluvial geomorphologist, ESA), Lorraine Flint (hydrogeologist, USGS), Robert Leidy (fisheries biologist, US EPA), Bruce Orr (riparian ecologist, Stillwater Sciences), and Steve Rottenborn (wildlife biologist, HT Harvey). The moderator for the discussion was Caitlin Sweeney (San Francisco Estuary Partnership). The audience, which included representatives from local partner organizations as well as state and federal regulatory agencies responsible for permitting projects, were active participants in the discussion and asked critical questions that helped clarify the measures being proposed. Taken together, the measures discussed at the workshop form the landscape concept.

This memorandum documents the key information from the Upper Penitencia Creek landscape concept workshop. Here, we provide a summary of the information presented at the workshop and an initial version of the landscape concept. A next step could include a more detailed description of the landscape characteristics and change over time, along with more information on the management measures and a refined landscape concept. This additional information will be useful to District staff as they work with local partners and regulatory agencies to develop a multi-benefit management approach for the creek and surrounding landscape over the short- and long-term.

2 Upper Penitencia Creek Overview Landscape Change Upper Penitencia Creek originates in the Diablo Range and then flows on an alluvial fan for approximately 4 miles through northeastern San Jose before discharging to Coyote Creek. In the early 1800s, the land adjacent to the creek was sycamore alluvial woodland, oak woodland, and oak savanna/grassland, and the creek emptied into a freshwater marsh/wet meadow adjacent to Coyote Creek. Dry season flow was intermittent and flood flows coming out of the canyon would spread out across the alluvial fan and recharge the local unconfined groundwater basin. Flood flows would also often connect Upper Penitencia Creek to Lower Penitencia Creek during the winter. The floodwaters would allow fish access to bottomland floodplain and freshwater marsh habitats, and would establish a migration corridor and aquatic habitat connectivity from Upper Penitencia Creek to Lower Penitencia Creek and the Bay. In addition, flood flows would deliver fine and coarse sediment from the upstream canyons that would help maintain in-channel and floodplain habitats on the alluvial fan (Beller et al. 2012).

Over the past 200 years, the lands adjacent to the creek were claimed for ranching and agriculture, and then converted into an urban and suburban landscape. Currently, seventy-five percent of the valley floor adjacent to the creek is urbanized. In the mid-1800s, the lowest reach of Upper Penitencia Creek was channelized and redirected into Coyote Creek to improve drainage and allow for more arable land (Beller et al. 2012). Since the mid-20th century, the creek has had perennial dry season flow in most years due to imported water being discharged into the creek for groundwater recharge.

Historical (top) and Modern (bottom) habitat types along Upper Penitencia Creek.

3 Runoff is now more rapidly delivered to the creek during storm events by a storm drain network and flood flows are constrained by earthen berms along the lower reaches of the creek. Coarse sediment transported along the channel in the wet season now gets trapped under bridges and culverts, causing some localized flooding issues and impediments to fish and wildlife passage (Stillwater Sciences 2006). Due to changes in dry season hydrology and land management practices, riparian vegetation composition has changed considerably and is now generally denser than it was historically (DeJager and Martel 2006, Grossinger et al. 2006), with wider canopy width in some areas, even though floodplains are generally more confined.

Riparian density along Upper Penitencia Creek in 1939 (left) and in 2009 (right).

Despite these changes, hydrologic and ecological processes still support wildlife in Upper Penitencia Creek. The relatively undeveloped watershed upstream of the valley floor results in a relatively natural storm hydrograph and relatively high coarse sediment supply compared to other Santa Clara Valley streams, despite the presence of Cherry Flat Reservoir. The creek is home to a persisting stand of California sycamore (Platanus racemosa) trees, which were once extensive in Santa Clara County, but are now a rare cover type (Keeler-Wolf et al. 1996, Sawyer et al. 2009). The creek is also critical steelhead habitat, providing steelhead with a relatively continuous riparian corridor along one of the shortest routes to spawning areas in the South Bay (Leidy et al. 2005, Stillwater Sciences 2006, Leidy 2007). In addition to steelhead, the creek also provides habitat for other native aquatic species, including Pacific lamprey (Entosphenus tridentatus) and Sacramento sucker (Castomous occidentalis) (CDFG 2009, CDFW and SJSU 2013). The riparian corridor also provides a pathway by which a variety of mammals and birds such as bobcats (Felis rufus) and oak titmice (Baeolophus inornatus) can disperse from the Diablo Range westward into the urbanized Santa Clara Valley. Enhancements along the Upper Penitencia and Coyote creek corridors could potentially promote movement along Coyote Creek to the Bay (Bay Area Open Space Council 2011).

Flood Risk Management The land adjacent to Upper Penitencia Creek floods during large storm events, particularly in the lower reaches near the confluence with Coyote Creek. Since the 1950s, there have been several major flood events that caused considerable damage, with the largest occurring in April 1958 (approximately a 60-year flood event).

The District recently used a 2-dimensional hydraulic model (HEC-RAS 5.0) to examine current flooding extents for a range of flood flows and identify floodplain parcels that are the most vulnerable to flooding and associated damage. The modeling showed that there are nearly 9,000 parcels within the Upper Penitencia 100-year floodplain (i.e., the portion of the floodplain that has a 1-percent chance of any flooding in a given year). These parcels include hundreds of private residences, 26 schools, 3 fire stations, and 1 rehabilitation center (Elmwood Rehabilitation Center). Additionally, vital transportation infrastructure such as Berryessa BART station, Highway 680, and Valley Transportation Authority Light Rail lines and stations are potentially at risk. However, the large areas of open space along the channel— nearly 1,300 acres in total—could provide opportunities for storing floodwaters and decrease the potential for flood damage.

Modeled 100-year flood extent along Upper Penitencia Creek. (source: Santa Clara Valley Water District).

5 Groundwater Management The District manages groundwater throughout the Santa Clara Valley for potable use by nearly 2 million people that live and work in the region (SCVWD 2016a). In the first half of the 20th century, excessive groundwater withdrawal to support the growing population and increasing agricultural production caused land subsidence in the northern portion of the Valley. Nearly 13 feet of permanent subsidence had occurred in San Jose by 1970 (SCVWD 2016b). To address this subsidence, reservoirs were built and water imported to increase infiltration into the groundwater basins, thereby helping maintain sustainable groundwater levels and halt permanent land subsidence. Upper Penitencia receives imported water from the State Water Project via the South Photo: Scott Dusterhoff Bay Aqueduct, mostly during the summer months. Water Groundwater recharge ponds adjacent deliveries are variable and depend on the water year type to Upper Penitencia Creek. and State Water Project operations. When water is available, it is stored within the Bob Gross Groundwater Recharge Ponds and then released into Upper Penitencia Creek during the summer months after natural creek flow recedes. The released flows are infiltrated into the groundwater basin through the creek bed between the ponds outfall and around the Mabury Road bridge crossing over 2 miles downstream. On average, about one-third of total groundwater recharge for this system is through instream recharge, while the remaining two-thirds is through percolation ponds (SCVWD 2016b).

Habitat and Water Quality Upper Penitencia Creek provides habitat for a diverse set of native and non-native plants, fish, and wildlife that are well adapted to the creek’s high seasonal and interannual flow variability. The rural Upper Penitencia Creek watershed supports California tiger salamander (Ambystoma californiense), California red- legged frog (Rana aurora draytonii), Photo: Melissa Moore and western pond turtle (Actinemys marmorata). Photo: Melissa Moore Adult steelhead trout Common and special status fish species in (Oncorhynchus mykiss) Upper Penitencia Creek include riffle and prickly sculpin (Cottus gulosus, C. asper), Sacramento sucker, steelhead trout, and Pacific lamprey.

Photo: Melissa Moore The California Department of Fish and Wildlife has conducted steelhead Pacific lamprey genetic analyses, steelhead and lamprey spawning surveys, and other (Entosphenus tridentatus) aquatic inventories in Upper Penitencia Creek (e.g., CDFG 2009, CDFW and SJSU 2013). Their work has shown low but consistent steelhead use of the creek corridor since they began surveying in 2007.

6 The creek riparian corridor also supports non-native amphibians (e.g., bullfrog (Rana catesbeiana)) and reptiles (red-eared sliders (Trachemys scripta elegans) and painted turtles (Chrysemys picta)), as well as native (e.g., oak titmouse) and non-native birds, and mammals such as bats (e.g., Pacific pallid bat (Antrozous pallidus pacificus)), coyotes (Canis latrans) and bobcats.

The Santa Clara Valley Urban Runoff Pollution Prevention Program (SCVURPPP 2014, 2015) reported poor biological conditions in Upper Penitencia during creek status monitoring in 2012 and 2013 and identified increased temperatures, altered flow regime, altered physical habitat, reduced dissolved oxygen, and the addition of nutrients and pesticides as potential factors explaining conditions in the creek. As a result, a bioassessment program was initiated in 2016 for Upper Penitencia Creek, including water quality, benthic macroinvertebrate (BMI) and algae surveys to monitor conditions more fully (SCVURPPP 2017). This study concluded that anthropogenic sources of poor conditions in the ephemeral segment of the creek are likely associated in part with diversions from the percolation ponds to the channel.

Recreation and Education The relatively extensive area of parks, trails, and open spaces along Upper Penitencia Creek provides local and regional residents opportunities for enjoyment of outdoor amenities including hiking, picnicking, bicycling, and wildlife viewing. The public land along the creek between Alum Rock Park and Coyote Creek is subject to a tri-party agreement among the County of Santa Clara, the City of San Jose, and the District, which allows and encourages use of the creek corridor for recreation, water conservation, and flood management. The City and County parks along the creek cover over 200 acres and contain amenities such as

Photo: Amy Richey ponds, playgrounds, and public restrooms. The Master PenitenciaPenitencia Creek Creek Park Parknear thenear Wildlife the Wildlife Center Center of Silicon of Silicon Valley. Valley. Plan for the Penitencia Creek County Park (1977) was developed with assistance from the two neighboring school districts, indicating the strong collaboration among the tri-party agreement partners. The Upper Penitencia Creek Trail runs along the creek from Dorel Drive approximately 3 miles downstream to King Road. The well-used trail is operated by the City of San Jose and connects the array of parks along the creek, from Noble Park down to Penitencia Creek Gardens.

Management Recommendations from the Science Advisors Drawing on the information given in the workshop presentations and subsequent discussions, Hub members and workshop participants discussed a suite of management recommendations during an afternoon brainstorm session. The Hub’s recommendations focused on holistic landscape management actions that benefit people and wildlife, and those that will enhance resiliency to changing climatic conditions. Here we provide a high level summary of the Hub recommendations discussed, with supporting information regarding key considerations for each recommendation, and the associated landscape concept with actions for discrete reaches of the creek.

Support Physical Drivers of Ecological Function Management actions should support physical processes, such as sediment transport and groundwater recharge, which in turn support key ecological functions such as food web support.

Focus on the watershed scale when considering sediment management. Managing the supply of fine and coarse sediment to the channel impacts flood management as well as in- channel habitat. For example, decreasing the total sediment supply can help maintain a high flood flow capacity in some reaches but also decrease spawning and rearing habitat for native steelhead. Therefore, both should be considered when developing a watershed-scale sediment management plan that addresses multiple objectives. Example approaches could include replacing bridge culverts with bridge spans that allow Photo: Amy Richey sediment to move more freely, or analyzing grazing and road Restored reach adjacent to the patterns in the upper watershed for effects on fine sediments. Berryessa BART station.

Manage imported water to be more ecologically beneficial. The State Water Project water supply can be unpredictable from year to year, and may change considerably in the future. The supply is very dependent on the amount of wintertime precipitation, and operations lie mostly outside the control of the District. Currently, the creek bed is used as a recharge facility during summer months, which has effects on instream water quality and biota, such as allowing persistence of non-native warm- water fish. Flows could be released in a manner that better supports native fish and riparian vegetation while still meeting Photo: Steve Thompson local water supply needs.

Nuttall’s woodpecker (Picioides nuttallii)

8 Support Habitat for Native Wildlife. The District and its partners have the opportunity to take an integrated ecosystem perspective that can balance wildlife, flood risk management, and recreation in the Upper Penitencia Creek corridor. There is potential to support natural streamflow and sediment transport, and enhance habitat for native plants and animals.

Enhance wildlife habitat patches and connectivity with corridors and nodes. There is an opportunity to improve functional connectivity for wildlife to support greater species diversity and resilience to climate change (Heller and Zavaleta 2009). Habitat can be enhanced within ‘nodes,’ larger areas that can support a variety of habitat functions for wildlife, while connectivity between nodes can be achieved with narrower wildlife-friendly riparian corridors (Koen et al. 2014). Management tactics within

Photo: Amy Richey nodes could include replacing non-native trees with natives Photo: Amy Richey such as oaks, willows and sycamores, expanding wooded areas, planting more multi-layered vegetation, and making room for California sycamore (Platanus racemosa) wildlife by excluding human uses from certain areas, for example, by moving trails away from the creek on one side.

Enhance steelhead habitat. There are opportunities to improve creek flow and sediment management to benefit steelhead. For example, Cherry Flat Reservoir releases could be managed to improve dry season water temperatures in the creek’s bedrock reaches, thereby benefiting rearing steelhead as well as other native fish species.

Enhance urban ecology. Sycamores, oaks, and other native trees could be planted throughout the urban areas adjacent to the creek to expand feeding and migration habitat for native birds (e.g., Acorn woodpecker (Melanerpes formicivorus)) and mammals (e.g., bats). This could include plantings in parks and other public open space areas as well as in yards and gardens of private residences, which could be incentivized through subsidies and rebate programs.

Manage Flood Risk and Seek Opportunities for Floodplain Enhancements It may be possible for the District and its partners to create and support landscape configurations that enhance both flood protection and habitats in the Upper Penitencia watershed.

Implement Low Impact Development (LID). Incorporating LID elements into streetscapes and other urban developments would slow, sink, and filter surface waters before entry into the river and stormwater systems, help recharge groundwater, and provide neighborhood and habitat amenities. LID elements that should be considered include rain gardens, vegetated drainage swales, and permeable pavement.

Consider variable riparian widths. The widths of riparian areas protected from development encroachment could be determined based on desired riparian function, such as surface water Photo: Amy Richey filtration, stream shading, habitat. Mixed riparian vegetation along Upper Penitencia Creek near Mabury Road There are new tools that can be used to help the District and its partners to determine riparian functional width along the creek (e.g., the Riparian Zone Estimator Tool (RipZET)).

Expand flood storage capacity. Current flood storage capacity along the creek could be expanded by increasing the area of existing open space next to the creek that regularly floods. Open space areas such as public parks and school athletic fields could be configured to store wintertime flood flows that then infiltrate into the underlying groundwater basin.

Envision and Prepare for Future Conditions For the San Francisco Bay Area, climate models suggest that in 50 years, there may be an increase in precipitation variability and large storm event frequency (Flint and Flint 2012). Multi-benefit management strategies need to account for this uncertainty in the Santa Clara Valley’s water future.

Conduct Scenario Planning. Use models to assess runoff, flow discharge, flow stage and velocity, and sediment transport for a suite of management scenarios and climate predictions. The output can be used to spark discussions among stakeholders regarding the range of options that meet management objectives and promote landscape resilience. Engaging local stakeholders early in scenario planning can reveal tradeoffs and optimize ecological and economic outcomes (Lester et al. 2013).

Invest in Low Impact Development. In addition to helping filter runoff and recharge groundwater, LID elements can slow runoff and help decrease the time to reach peak storm discharge and the peak discharge value (i.e., decrease storm ‘flashiness’), which would help maintain overall channel stability and prevent excess erosion.

10 UPPER PENITENCIA CREEK

PRELIMINARY LANDSCAPE CONCEPT

680

Berryessa Rd. Coyote Creek Coyote

Upper Penitencia Creek

COYOTE CREEK REACH 1 REACHES 2 & 3 REACHES 4 & 5

Reach 1 Reaches 2 and 3 CONSIDERATIONS FOR THE ENTIRE (Coyote Creek to King Rd.) (King Rd. to N. Capitol Ave.) VALLEY FLOOR (REACHES 1-7): At the confluence with Coyote Creek, These reaches include the Mabury The urbanized reaches within the the lower portion of the reach forms Road crossing and bypass channel, and valley floor contain nearly 1300 a series of pools and riffles within a the Highway 680 crossing. County Park acres of public or open space. confined channel that flows through and Mabury Park attract picnickers, an area that is almost entirely paved. hikers, and walkers. This reach dries in • Utilize Low Impact Development The upper portion of the reach is the summer until flows are augmented techniques to slow stormwater, ephemeral and has recently been with imported water. recharge groundwater, restored with habitat enhancements • Consider converting Mabury bypass reduce pollution, and provide for salmonids. channel to a low-flow channel and neighborhood and habitat • Reconfigure floodplain at the planting riparian vegetation to improve amenities confluence of Upper Penitencia and fish habitat Coyote Creeks to maximize habitat • Increase flood storage capacity • Manage non-native woody connectivity for wildlife migration within open spaces vegetation in favor of native and dispersal • Improve conveyance and wildlife trees, including California • Consider variable-width setbacks connectivity under Jackson Avenue sycamore to enhance wildlife connectivity and and I-680, enhance bridge areas with • Plant native shrubs and flood storage mosaic of native plantings herbaceous vegetation where • Design bank slopes and manage • Plant native understory vegetation appropriate vegetation to enhance in-channel and consider restricting public wildlife migration and dispersal access along one side of the creek to • Daylight storm drains and set support wildlife back hardscapes from stream corridor as feasible. • Re-consider sediment removal policy under Highway 680 bridge, which currently calls for hauling coarse sediment off site Piedmont Rd.

REACHES 4 & 5 REACHES 6 & 7 UPPER REACHES

Reaches 4 & 5 Reaches 6 & 7 Upper Reaches (N. Capitol Ave. to Piedmont Rd.) (Piedmont Rd. to Hills) (Hills to Watershed Boundary) These reaches contain two schools, These reaches generally flow The upper watershed of Upper a nature center, and Penitencia Creek perennially upstream of the Bob Penitencia Creek mainly drains Park. Several roads cross over the Gross Ponds, and contain a higher rangeland, with few roads. Current creek within these reaches. These concentration of California sycamore land use is primarily cattle grazing. reaches dry down in the summer until than other reaches. Cherry Flat Reservoir dams a flows are augmented with imported minority of the watershed, allowing water. • Explore reconfiguration of Penitencia for nearly natural sediment transport Creek Road for flood protection of within these reaches. • Enhance terrestrial habitat properties to the south structure for wildlife within open • Sediment output may increase spaces • Replace non-native trees with native with future climatic changes trees so modifying roads and grazing • Improve wildlife passage and regime upstream may benefit • Consider replacing small bridges native plant assemblages instream conditions for and driveway crossings with higher surrounding and under bridges salmonids and native fishes and culverts capacity structures • Revisit Cherry Flat Reservoir • Enhance habitat quality of Bob Gross • Increase flood storage potential of operations and management Ponds area for terrestrial wildlife open spaces and parking lots opportunities in the context of • Consider ways to use Bob Gross fisheries support Ponds as floodplain features to increase flood storage • Maintain fish ladder and/or improve its function Next Steps The landscape concept for Upper Penitencia Creek presented here contains preliminary ideas developed during the one-day workshop by the Science Advisory Hub in coordination with the District, SFEI-ASC, and workshop participants. Ultimately, these concepts will need thorough analyses to explore their feasibility, costs versus benefits, and their overall effectiveness at helping to meet flood management and other management objectives.

Additionally, there are challenges, constraints and knowledge gaps present along the creek corridor, including: . Implications of managing the Mabury bypass channel differently, including potential impacts to riparian cover and fish passage . Cherry Flat Reservoir operations in relation to potential management of instream conditions for fish . Implications of use of groundwater supply ponds for flood storage . Impacts of changes in management to current human uses of parklands, including recreation and homeless encampments . Lack of long-term stream temperature and sediment processes data

The following topics could be explored during future analyses: . Key ecosystem drivers . Climate change impacts . Long-term sediment dynamics . Optimal size and arrangements for habitat nodes and corridors . Ways to improve instream habitat

conditions for wildlife, including support Photo: Amy Richey for salmonids Photo: Amy Richey . Shallow groundwater monitoring Upper Penitencia Creek near the Noble Ave. Bridge. to guide habitat enhancement and flood control basins

Flood risk challenges are great on Upper Penitencia Creek, but the potential for improved flood management and habitat enhancement benefits is even greater. Tradeoffs will be inevitable, so an essential next step is to engage with a broader group of key stakeholders in the watershed, including the City of San Jose, Santa Clara County Parks and Recreation, and members of the regulatory community.

Acknowledgments We would like to give special thanks to Caitlin Sweeney for moderating the workshop, to the Science Hub members for providing their ideas, and to the Santa Clara Valley Water District staff who made the workshop possible, and provided critical information during the pre-workshop creek field visit and during the workshop. District staff includes Sara Duckler, Jim Manitakos, Carole Fisher, Brian Mendenhall, Gabriel Vallin, Ben Hwang, Afshin Rouhani, Melissa Moore, Chad Grande, and Aaron Baker.

14 Literature Cited

Bay Area Open Space Council. 2011. The Conservation Lands Network: San Francisco Bay Area Upland Habitat Goals Project Report. Berkeley, CA.

Beller, E., Grossinger, R., Nicholson, M., Salomon M. 2012. Upper Penitencia Creek Historical Ecology Assessment. A report of SFEI’s Historical Ecology Program, SFEI Publication #664, San Francisco Estuary Institute, Richmond, CA.

CDFG. 2009. California Department of Fish and Game. Memorandum. Upper Penitencia Creek Fish Sampling. August 27, 2009.

CDFW and SJSU. 2013. Upper Penitencia Creek Fish Resources in 2013. Michelle Leicester, CDFW and Jerry Smith, Department of Biological Sciences, San Jose State University. December 28, 2013.

DeJager, B. and Martel, D. 2006. Upper Penitencia Creek Feasibility Study Draft Functional Assessment. U.S. Army Corps of Engineers, San Francisco District. 29 August.

Flint, L.E., and Flint, A.L. 2012. Simulation of climate change in San Francisco Bay Basins, California: Case studies in the Russian River Valley and Santa Cruz Mountains: U.S. Geological Survey Scientific Investigations Report 2012–5132, 55 p.

Grossinger, R.M., R.A. Askevold, C.J. Striplen, E. Brewster, S. Pearce, K.N. Larned, L.J. McKee, and J.N. Collins, 2006. Coyote Creek Watershed Historical Ecology Study: Historical Condition, Landscape Change, and Restoration Potential in the Eastern Santa Clara Valley, California. Prepared for the Santa Clara Valley Water District. A Report of SFEI’s Historical Ecology, Watersheds, and Wetlands Science Programs, SFEI Publication 426, San Francisco Estuary Institute, Oakland, CA.

Heller, N.E. and Zavaleta, E.S., 2009. Biodiversity management in the face of climate change: a review of 22 years of recommendations. Biological conservation, 142(1), pp.14-32.

Keeler-Wolf, T., K. Lewis, and C. Roye. 1996. The definition and location of Sycamore Alluvial Woodland in California. State of California, Resources Agency, California Department of Fish and Game, Sacramento.

Koen, E. L., Bowman, J., Sadowski, C. and Walpole, A. A. (2014), Landscape connectivity for wildlife: development and validation of multispecies linkage maps. Methods Ecol Evol, 5: 626–633.

Leidy, R.A. 2007. Ecology, Assemblage Structure, Distribution, and Status of Fishes in Streams Tributary to the San Francisco Estuary, California. San Francisco Estuary Institute Contribution No. 530.

15 Leidy, R.A., G.S. Becker, B.N. Harvey. 2005. Historical distribution and current status of steelhead/ rainbow trout (Oncorhynchus mykiss) in streams of the San Francisco Estuary, California. Center for Ecosystem Management and Restoration, Oakland, CA.

Lester S., Costello C., Halpern B., Gaines S., White C., and Barth J. 2013. Evaluating tradeoffs among ecosystem services to inform marine spatial planning. Marine Policy. 2013 March 31;38:80-9.

Sawyer, J. O., T. Keeler-Wolf, and J. M. Evens. 2009. A Manual of California Vegetation. Second edition. California Native Plant Society Press, Sacramento.

SCVURPPP. 2014. Santa Clara Valley Urban Runoff Pollution Prevention Program. Watershed Monitoring and Assessment Program. Integrated Monitoring Report, Part A, Water Quality Monitoring Water Years 2012 and 2013 (October 2011-September 2013). March 15.

SCVURPPP. 2015. Santa Clara Valley Urban Runoff Pollution Prevention Program. Watershed Monitoring and Assessment Program. Integrated Monitoring Report, Water Quality Monitoring Water Year 2014 and 2013 (October 2013-September 2014). March 15.

SCVURPPP. 2017. Santa Clara Valley Urban Runoff Pollution Prevention Program. Watershed Monitoring and Assessment Program. Upper Penitencia Creek Stressor/Source Identification Project, Water Year 2016. March 31.

SCVWD. 2008. Santa Clara Valley Water District. Mid-Coyote Creek Baseline Flood Protection Project. Baseline Fisheries Monitoring Report. Year 2. Watershed Management Division. April 5, 2009.

SCVWD 2016a. Santa Clara Valley Water District 2015 Urban Water Management Plan. Lead: T. Hemmeter, et al. May 2016.

SCVWD 2016b. Santa Clara Valley Water District 2016 Groundwater Management Plan, Santa Clara and Llagas Subbasins. Leads: B. Kassab and G. Cook. November 2016.

Stillwater Sciences. 2006. Upper Penitencia Creek Limiting Factors Analysis Final Technical Report Prepared for Santa Clara Valley Urban Runoff Pollution Prevention Program (Program Manager, EOA, Inc.).

Thompson, Steve. 2017. Nuttall’s Woodpecker (photo). Attribution-NonCommercial-ShareAlike 2.0 Generic (CC BY-NC-SA 2.0). Downloaded from: https://www.flickr.com/photos/srdt6458/34653935520/

16 Appendix A Workshop Attendees

Don Arnold, SCVWD Aaron Baker, CVWD Carol Boland, City of San Jose Setenay Bozkurt-Frucht, RWQCB Brett Calhoun, SCVWD Jennifer Castillo, SCVWD Andy Collison, ESA (Hub Member) Sara Duckler, SCVWD Scott Dusterhoff, SFEI Lorraine Flint, USGS (Hub Member) Carole Foster, SCVWD Errol Gabrielson, SCVWD Vince Gin, SCVWD Susan Glendening, State Water Board Chad Grande, SCVWD Robin Grossinger, SFEI Ben Hwang, SCVWD Hieu Huynh, SCVWD Rob Leidy, EPA (Hub Member) James Manitakos, SCVWD Michael Martin, SCVWD Brian Mendenhall, SCVWD John McKeon, NMFS Katie McKnight, SFEI Dave Mitchell, CSJ-PRNS Melissa Moore, SCVWD Katie Muller, SCVWD Bruce Orr, Stillwater Sciences (Hub Member) Paul Randall, SCVURPPP Amy Richey, SFEI Steve Rottenborn, HT Harvey (Hub Member) Afshin Rouhani, SCVWD Jake Smith, SCVOSA Gary Stern, NMFS Kirsten Struve, CVWD Caitlin Sweeney, SFEP (Moderator) Tim Tidwell, SCVWD Andrew Trent, NMFS

17 Appendix B Workshop Presentation Slides

18 Landscape Workshops Upper Penitencia Creek Landscape Concept Workshop • Novato Baylands (2015)

• Lower Walnut Creek (2016)

• Calabazas‐San Tomas Aquino‐Pond A8 (planned May 2017)

Multi‐benefit Goals Landscape Workshops • multi‐project scale • multi‐benefit (particularly flood protection and sediment management) • regional + local expertise • environmental science + engineering • eye towards regulatory drivers • long‐term resilience; incorporate climate change • pastpresentfuture approach • One Water and Resilient Silicon Valley

OUTLINE UPPER PENITENCIA CREEK Upper Penitencia Creek Workshop LANDSCAPE: March 13, 2017 1. Setting Historical functions and change‐through‐time 2. Historical Landscape Conditions

3. Timeline of Landscape and Channel Change

4. Contemporary Conditions

5. Change Analysis and Landscape Parameters

6. Summary

1 UPPER PENITENCIA WATERSHED REGIONAL CONTEXT

WATERSHED BOUNDARY

HILLS Cherry Flat Reservoir

San Jose Alum Rock Park

VALLEY FLOOR

NAIP 2009

UPPER REACH LOWER REACH

Piedmont Middle School/Penitencia Upper Penitencia Creek Park Water Treatment Plant Cherry Flat Reservoir ~4 miles upstream East Side Union San Jose High School Groundwater Recharge Municipal District Ponds Golf Penitencia Piedmont Middle Course Creek School/Penitencia County Creek Park Alum Rock Park Park

Toyon San Jose Elementary Flea School Market San Jose Independence Country Club High School

REGIONAL CONTEXT REGIONAL CONTEXT

ALLUVIAL FAN OF UPPER PENITENCIA CREEK QUATERNARY STREAM LEVEES, SANTA CLARA VALLEY

APPROX. BOUNDARY

CONFINED UNCONFINED ZONE INACTIVE STREAM LEVEE ZONE INACTIVE STREAM LEVEE

ACTIVE STREAM LEVEE ACTIVE STREAM LEVEE

UNCONFINED ZONE CONFINED ZONE

SCALE 1 : 50,000 SCALE 1 : 50,000 ELEVATION: 30 ft 290 ft Source: Kenneth R. Lajoie (March 2002)

2 STUDY AREA OUTLINE

1. Setting

2. Historical Landscape Conditions

3. Timeline of Landscape and Channel Change

4. Contemporary Conditions

5. Change Analysis and Landscape Parameters

6. Summary

PREVIOUS STUDIES

Photographs

Maps

Texts

THEN AND NOW THEN AND NOW

CONCEPTUAL MODEL: Historical CONCEPTUAL MODEL: Contemporary

CONCEPTUAL MODEL: Contemporary

3 HISTORICAL CHANNEL AND HABITATS

Noble Ln. Noble Ln.

Highway 680 Highway 680

Oak Woodland Oak savanna/Grassland Lundy Ave. Lundy Ave.

Willow Grove Wet Meadow Freshwater Marsh

Riparian Woodland

Modern Aerial Imagery; Historical Habitats

HISTORICAL CHANNEL AND HABITATS HISTORICAL CHANNEL AND HABITATS

Noble Ln. Noble Ln.

Highway 680 Highway 680

Oak Woodland Oak Oak Woodland Oak savanna/Grassland savanna/Grassland Lundy Ave. Lundy Ave.

Willow Grove Willow Grove Wet Meadow Wet Meadow Freshwater Marsh Freshwater Marsh

Riparian Woodland Riparian Woodland

Modern Aerial Imagery; Historical Habitats Modern Aerial Imagery, Modern Channels; Historical Habitats

HISTORICAL: HABITAT TYPES HISTORICAL: FEATURES

ALKALI MEADOW (low concentration) WILLOW GROVE

OAK WET SAVANNA/ MEADOW GRASSLAND

OAK WOODLAND

BAR WITH WET OAK RIPARIAN MEADOW WOODLAND WOODLAND

FRESHWATER MARSH

WET SYCAMORE GROVE MEADOW ALKALI MEADOW SEASONAL LAKE / POND

4 HISTORICAL: FEATURES HISTORICAL: FLOW PATTERNS

OUTFLOW TO TIDAL MARSH AND SAN FRANCISCO BAY

SEASONALLY CONNECTED FLOW DURING RAINY REPLENISHED DRY PERIODS GROUNDWATER

WETLANDS/ FLOODING

NATURAL ALLUVIAL FAN

PERIODIC CONNECTIONS BETWEEN FLUVIAL NATURAL LEVEE CHANNEL AND FLOODPLAIN

HISTORICAL: WILDLIFE CONNECTIVITY HISTORICAL: GROUNDWATER

OUTFLOW TO TIDAL MARSH AND SAN FRANCISCO BAY APPROX. BOUNDARY

SEASONAL CONNECTION FOSTERED WILDLIFE CONNECTIVITY TO BAY CONFINED UNCONFINED SEASONAL BACKWATERS SERVED AS FISH HABITAT ZONE ZONE

SPREADING SURFACE WATERS LED FISH TO FORAGE IN BOTTOMLAND FLOODPLAIN HABITATS

TRANSITION BETWEEN ECOTONES FOR AMPHIBIANS AND TERRESTRIAL WILDLIFE

OUTLINE TIMELINE: EARLY TO MID 1800s

1. Setting

2. Historical Landscape Conditions

3. Timeline of Landscape and Channel Change

4. Contemporary Conditions

5. Change Analysis and Landscape Parameters

6. Summary

Ranching, farming, ‘milpitas’ < 1800 Farming, ranching

5 TIMELINE: MID TO LATE 1800s TIMELINE: LATE 1800s to EARLY 1900s

1852: Connection to Coyote

“In that year a settler dug a ditch and built fences, and in the fall the creek sent down its waters, which entered the ditch and continued on, cutting a channel through which the waters were afterward discharged.”

(Sawyer 1922, History of Santa Clara County, pp 302) Late 1800s- Channel Modifications Early 1900s for Agriculture 1880s: Ditching for Irrigation 1852 Connection to 1852 Connection to Coyote “In 1889 George W. Page developed … the Coyote Auzerais Ditch on the Penitencia creek.” < 1800 Farming, ranching (Payne 1987, Santa Clara County: Harvest of change, pp137) < 1800 Farming, ranching

TIMELINE: LATE 1800s to EARLY 1900s TIMELINE: 1920s – 1950s

Continued Diversions for Irrigation, Groundwater Pumping 1920s- Groundwater Pumping, 1950s Suburbanization

Late 1800s- Channel Late 1800s- Channel Early 1900s Modifications for Early 1900s Modifications for Roads and Railroads Roads and Railroads

Late 1800s- Channel Modifications “ ‘several small dams’ along the creek divert Late 1800s- Channel Modifications Early 1900s for Agriculture water to adjoining farms. Diversions appear Early 1900s for Agriculture to have principally occurred during the wet 1852 Connection to season.” 1852 Connection to Coyote Coyote 1880s: Roads and Railroads (Tibbetts and Kieffer 1921)

< 1800 Farming, ranching < 1800 Farming, ranching

TIMELINE: 1950s ‐ 1980s TIMELINE: 1980s to present

UPPER PEN. WATER Suburbanization Water Infrastructure TREATMENT PLANT SOUTH BAY AQUEDUCT “A majority of the area was urbanized by 1980.” TERMINAL TANK (DeJager and Martel, Draft Functional Assessment, pp 6) 1950s- Water Infrastructure PENITENCIA 1970s PARK POND HELMSLEY Groundwater Groundwater 1920s- POND 1920s- Pumping, Pumping, 1950s 1950s Suburbanization Suburbanization

Late 1800s- Channel Late 1800s- Channel Early 1900s Modifications for Early 1900s Modifications for Roads and Railroads Roads and Railroads

Late 1800s- Channel Modifications Late 1800s- Channel Modifications Early 1900s for Agriculture COUNTY PARK POND Early 1900s for Agriculture

MABURY POND 1852 Connection to 1852 Connection to Coyote Coyote

< 1800 Farming, ranching < 1800 Farming, ranching MIGUELITA CREEK

6 TIMELINE: 1980s to present OUTLINE

1980s- Several Major Floods 1. Setting Flood Events present

March 1982 at King Road Bridge (10 year flood) 1950s- Water Infrastructure 1970s 2. Historical Landscape Conditions

1920s- Groundwater Pumping, 1950s 3. Timeline of Landscape and Channel Change Suburbanization

Late 1800s- Channel Early 1900s Modifications for 4. Contemporary Conditions Roads and Railroads January 1983 at San Jose Flea Market (5 year flood) Late 1800s- Channel Modifications Early 1900s for Agriculture 5. Change Analysis and Landscape Parameters

1852 Connection to Coyote 6. Summary

< 1800 Farming, ranching

CONTEMPORARY: LAND COVER TYPES CONTEMPORARY: FLOW PATTERNS

75% OF THE VALLEY FLOOR WITHIN THE UPPER PENITENCIA WATERSHED IS URBANIZED

GRASSLAND / OAK RESIDENTIAL / SAVANNA FARMLAND WOODLAND DEVELOPED

NO LONGER FLOWS INTO SEASONAL COASTAL WETLAND FRESHWATER SCRUB MARSH DIRECT POND OR DISCHARGE RESERVOIR INTO COYOTE CREEK (c. 1850) RIPARIAN WOODLAND FARMLAND

PARK OR RESIDENTIAL / GOLF COURSE DEVELOPED

CONTEMPORARY: FLOW PATTERNS CONTEMPORARY: SEDIMENT TRANSPORT

recreational water weir diversion CHANNEL MODIFICATIONS facility & ALTER HYDRAULICS & fish ladder MORPHOLOGY

gaging weir weir low flow critical vehicle riffle crossing CULVERTS AND STORM DRAINS gaging weir ALTER FLOW PATHWAYS

EARTHEN BERMS culvert water diversion facility & fish FEMA 100‐YEAR FLOOD EXTENT ladder (2016)

7 CONTEMPORARY: SEDIMENT TRANSPORT CONTEMPORARY: GROUNDWATER

STRUCTURES & CHANNEL DIVERSIONS AFFECT SEDIMENT TRANSPORT AND FISH PASSAGE

UPPER PENITENCIA CONTINUES TO BE AN IMPORTANT SEDIMENT SOURCE FOR LOWER REACHES BUT THIS ALSO CAUSES A NEGATIVE IMPACT OF SEDIMENT BUILD‐UP AT THE CONFLUENCE

CONTEMPORARY: GROUNDWATER CONTEMPORARY: WILDLIFE CONNECTIVITY

APPROX. CONFINED‐ UNCONFINED BOUNDARY

Source: Summary data for ARCO #0674 (T0608533095) (from GeoTracker website) Source: Critical Linkages Map (2013) http://www.bayarealands.org/mapsdata.html

CONTEMPORARY: WILDLIFE CONNECTIVITY CONTEMPORARY: WILDLIFE CONNECTIVITY

Upper

Noble Ln. Reaches Rearing & Noble Ln. Breeding & Highway 680 Spawnin feeding for Highway 680 rearing for Lower g & cover native amphibians fishes & reptiles Reaches Lundy Ave. Lundy Ave. Rearing & feeding for anadromou s fishes

Lamprey, California Tiger Salamander, Western Toad. Photos: Melissa Moore

8 CONTEMPORARY: WILDLIFE CONNECTIVITY FUTURE: CLIMATE CHANGE (2012) Source: Flint and Flint

Models project…

Movement • Warming air temps & foraging Noble Ln. Highway 680 for • Longer and drier summers mammals & • Increased dry season birds Lundy Ave. evapotranspiration • Increased water deficit • Potential increased precipitation Courtesy Dipika Bhattacharya variability

Need to manage for an uncertain water future

Yellow‐Breasted Chat. Photo: Bobcat. Photo: Tanya Diamond Scott Walker Source: Flint and Flint. 2012. Simulation of Climate Change in San Francisco Bay Basins, California: Case Studies in the Russian River Valley and Santa Cruz Mountains

OUTLINE LANDSCAPE PARAMETERS

1. Setting Flow Patterns 2. Historical Landscape Conditions Channel Planform 3. Timeline of Landscape and Channel Change Habitat Type 4. Contemporary Conditions Riparian Veg Composition 5. Change Analysis and Landscape Parameters Riparian Density & Width 6. Summary

Dry Season Flow Patterns Channel Planform

Channel Length Channel Length Surface Subsurface (miles) Intermittent Perennial (miles) Channel Storm Drain

Historical 3.9 0 Historical 3.9 0

Modern 1.9 3.0 Modern 4.9 12.7

6 20 18 5 16 14 4 12 Subsurface Storm 3 Perennial 10 Drain Intermittent 8 Surface Channel 2 6 Channel length (mi) Channel length (mi) 1 4 2 0 0 Historical Modern Historical Modern

9 Habitat Type Riparian Vegetation Composition

3500

Urban Open / Other

3000 Urban

Perennial Noble Ln. 2500 Freshwater Pond Wet or Alkali Meadow Remnant 2000 Valley Freshwater Marsh sycamores acres Riparian 1500 Stream present; Channel Riparian conversion to Nonnative Vegetation wetter spp 1000 Riparian Native Vegetation

Oak Woodland 500

Grassland

0 Historical Modern

Riparian Density & Width OUTLINE

1939 2009

VEGETATION IS 1. Setting Upper Alluvial GENERALLY MORE Fan DENSE THAN HISTORICALLY 2. Historical Landscape Conditions

3. Timeline of Landscape and Channel Change CANOPY WIDTH IS GREATER IN SOME Lower Alluvial AREAS; BUT Fan FLOODPLAINS ARE MORE CONFINED 4. Contemporary Conditions

5. Change Analysis and Landscape Parameters

WIDTH AND DENSITY Wetland Reach IS LIKELY MUCH REDUCED FROM THE 6. Summary 1850s

CONSIDERATIONS CONSIDERATIONS Persisting Hydrologic Functions Persisting Hydrologic Functions • Coarse sediment supply and in‐channel storage • Coarse sediment supply and in‐channel storage • Streamflow (storm and low‐flow, ephemeral and perennial) • Relatively undammed and natural hydrograph • Channel‐overbank connections (but storm and low‐flow, ephemeral vs. • Channelization at Coyote Creek confluence perennial) • GW/SW interactions • Potential for channel‐overbank connections Regionally Unique Habitats Ecological Features • Riparian species comp, density, structure • Sycamores/CSAW • Sycamores/CSAW • “Essential” Steelhead Stream (Becker et al. • Ecotones (riparian/oak savanna) 2007) • Native warm‐water fish Wildlife Connectivity Wildlife Connectivity • Fishes • Fishes • Amphibians, reptiles, birds,mammals • Amphibians, reptiles, birds,mammals

10 CONSIDERATIONS Persisting Hydrologic Functions • Coarse sediment supply and in‐channel storage • Streamflow (storm and low‐flow, ephemeral and perennial) • Channel‐overbank connections • Channelization at Coyote Creek confluence • GW/SW interactions Ecological Features QUESTIONS? • Riparian species comp, density, structure • Sycamores/CSAW • Ecotones (riparian/oak savanna) Wildlife Connectivity • Relatively continuous riparian corridor –short route for steelhead • Amphibians, reptiles, birds, mammals to Baylands resources • Potential ecotones (riparian<‐>oak savanna)

11 Upper Penitencia Flood Risk Upper Penitencia Watershed

Gabriel Vallin, Asc. Engineer Benjamin Hwang, Ast. Engineer

Project Area Design Flows

Storm Event Peak Flows (CFS) 43% 10% 0.5% 20% (5 4% (25 2% (50 1% (100 0.2% (500 (2.33 (10 (200 year)* year)* year) year) year) Location year)* year) year) Upper Pen @ Dorel Dr 400 900 1400 2300 3000 3800 4500 5600 Upper Pen @ Piedmont Rd 400 900 1400 2300 3000 3800 4600 5700 Upper Pen @ I‐ 680 400 900 1400 2300 3000 3800 4600 5600 Upper Pen U/S Coyote 400 900 1500 2400 3100 4000 4800 6000

USACOE Flood Risk Management Study USACOE Flood Risk Management Study

Existing Channel Capacities (need to update) History of Flooding in Upper Penitencia Creek

• Significant flooding has occurred in 1955, 1958, 1980, 1982, and 1983 • Lesser but more recent floods in 1986 and 1995 • Largest recorded flood in 1958 with an estimated peak flow of 3,730 CFS (approx. 1.7% annual chance exceedance event) USACOE Flood Risk Management Study

January 1983: (5-year flood Event) March 1982: (10-year flood event) Flooding at San Jose Flea Market Flooding at King Road Bridge

USACOE Flood Risk Management Study

1 Hydraulic Model Hydraulic Modeling – 2D Components HEC‐RAS 5.0 Terrain Map – 2006 County LiDAR

Hydraulic Modeling – 2D Components Flooding – Variable Storm Events

National Land Cover Database (NLCD) from USGS

Parcels Within 100 Year Floodplain Notable Facilities within the 100 Year Floodplain

Roughly 9,800 Notable Facilities within the parcels within 100 year floodplain include: Upper Penitencia’s • 33 Schools 100 year floodplain • 3 Fire stations Notable Transportation Infrastructure: • Berryessa BART Extension • Highway 680 • VTA Light Rail

2 February 2017 Storm Event “Historical” Flooding – February 2017

Bypass channel looking downstream from Cape Horn Upper Penitencia Creek abandoning the Drive main channel into the “bypass” between Jackson Ave. and King Rd. Main Breakout into bypass channel

Mabury & Educational Park Dr.

Breakout into “Bypass Channel” Breakout into County Park Pond

A Unique Setting…

1,295 acres of open space adjacent to Upper Penitencia Creek The End

3 SCVWD Water Supply Infrastructure Groundwater Recharge Ponds

• South Bay Aqueduct – feeds Penitencia Water • Bob Gross Ponds (SCVWD) – Reach 6 Penitencia Treatment Plant • Piedmont Ponds (SCVWD) – Reach 5 WTP

• Penitencia Park Ponds (CSJ) – Reach 5 • Penitencia Water Treatment Plant (WTP)– treats • Helmsley Pond, Upper and Lower Capitol Ponds, raw water to produce potable water, adjacent to Reaches 4 and 5 Reach 6 • County Pond (SCC) – Reach 2

• Water Diversions – upstream of Noble Ave • Mabury Pond – Reach 2 (Reach 7) and at Mabury Meander (Reach 2), Mabury Diversion feeds Mabury Pond and Overfelt Gardens ( CSJ Park)

1 Upper Penitencia Creek Native Fish Fauna California Aquatic Ecology

High annual seasonal variability in flows; native fish are adapted to hydrologic extremes

Of 124 native inland fishes (defined as those breeding in freshwater) 64% are endemic to the state, with 19% also found in Nevada or Oregon.

California has a unusually high proportion of anadromous (sea‐run taxa) (23%)

Upper Penitencia Creek has 2 andromous species, steelhead and lamprey

SCVWD Aquatic Ecology SCVWD Native Fish Distribution

Coyote Creek Watershed

Central Valley Subprovence (2d) center of speciation, with 35 native taxa, (16) endemic taxa

Fishes of Coyote Creek Steelhead Genetics

1 Steelhead Genetics Upper Penitencia Annual Surveys CDFW/SFSU Creek Annual aquatic inventory is conducted in Upper Penitencia Creek (2007‐present) Watershed evaluation; • Alum Rock Park, which receives its summer and fall stream flow from natural runoff, a small (< 500 acre‐foot) headwater reservoir • lower valley floor percolating reach, which receives South Bay Aqueduct water

SCVWD/NMFS Spawning Surveys SCVWD/NMFS Survey Results

• Surveys: 7 Upper Pen: 2 Arroyo Aguague Lower • 9 redds reach: Confluence of • 20 live O. mykiss the Coyote Creek ‐ Noble water • Redd density: 1.2/RM diversion @ RM 3.7 • 4 Pacific lamprey

Upper reach • 2 Pl redds (1 under Noble diversion & construction) ended at the natural barrier located at RM 6.8

Upper Penitencia Creek Lamprey Rearing

A Phylogeographic • Larval lamprey use the substrates of Upper Analysis of Penitencia Creek The Pacific • Spend approximately five years in Lamprey microphagus stage Entosphenus tridentatus USFWS ‐Collection locations depicted in red

2 Sycamore Alluvial Woodland Mapping and Water Quality Upper Penitencia Creek 2016 Regeneration Study

Santa Clara Valley Urban Runoff Pollution Prevention Program (Stressor ID Project)

Upper Penitencia Creek SSID (MRP 1.0) • Triggered by low biological condition scores in adjacent sites

Four Steps Provision C.8.d.i 1. Identify source 2. Evaluate control options 3. Implement control 4. Confirm reduction of cause

Upper Penitencia Creek Results - Biological Conditions

• What do the bugs tell us? – Fluctuating habitat conditions • BMI with short life cycles; Chironomids and black flies comprise over 90% of the BMI taxa at all sites in April/May; • More stable flow conditions at site 121 in June – Non-perennial flow (site 114) • Absence of both larval and adult life stages of Coleoptera taxa (beetles) and predator taxa – Perennial flow (site 121) • Presence of long-lived, predator and intolerant taxa

Upper Penitenica Creek Results - Biological Conditions Upper Penetencia Creek – Preliminary Conclusions

• What does the algae tell us? • Identify Source – No clear linkage – Evidence of more stressors at site 114 (both events) between stressor and • Greater proportion of taxa tolerant of fine sediment and biological condition dissolved salts (halobiontic). data – Response to nutrients at site 114 (June event) – Site 114 - Historically non-perennial; • Greater proportion of diatom taxa that utilize organic bound groundwater nitrogen (heterotrophic) percolation zone • Possible dispersal of algae from percolation ponds to the creek – Frequent changes in flow and water quality; both natural and managed (imported water)

DRAFT Do Not Cite or Quote

3 Upper Penetencia Creek – Preliminary Conclusions Reptiles and Amphibians

• Evaluate and Implement Control Options – Current study did not identify sources to control – Natural variability of flow during spring/summer – Some uncertainty in potential impacts to biological condition from imported water • Timing and magnitude of discharge from percolation ponds • Impacts associated with water quality (e.g., temperature) • Confirm Reduction of Cause – Difficult to evaluate flow related impacts; variable year to year

Upper Penitencia Creek Considerations for Birds and Mammals Management R

Spawning Lamprey

4 Recreation: SF Bay Basin Plan Fig. 2‐7a Beneficial Uses of Upper Penitencia Cr

San Francisco Bay Basin Plan (Regional Water Quality Control Board ) designates the following beneficial uses for Upper Penitencia Creek: Upper Penitencia Creek ‐ Water‐contact recreation (REC‐1) ‐ Non‐contact water recreation (REC‐2) ‐ Natural/artificial maintenance of surface water quality or quantity (FRSH) ‐ Groundwater recharge (GWR) ‐ Cold freshwater habitat (COLD) ‐ Fish migration (MIGR) ‐ Preservation of rare and endangered species (RARE): steelhead, chinook, CA red‐legged frog ‐ Fish spawning (SPWN) ‐ Warm freshwater habitat (WARM) ‐ Wildlife habitat (WILD)

Upper Penitencia Cr Joint Use Agrmnt Penitencia Creek County Park

• Agreement among City of San Jose, County of Santa Clara, and • 163 Acres, includes Penitencia Creek Gardens SCVWD; executed in 1981, renewed in 2007 for 25 years • Linear park and regional trail following creek alignment • Alum Rock Park (upstream terminus) to coyote Creek confluence (downstream terminus) • Hiking, picnicking, bicycling, walking dogs on leash wildlife viewing • Allow and encourages joint use of public lands in the creek corridor • Operated by Santa Clara County Parks for “parks, recreation, open space, flood management, and water conservation.” • Master Plan developed with assistance from East Side Union School District (SD) and Berryessa Union SD • Objectives include:

– “aesthetically pleasing flood control improvements” and

– “minimizing disturbance of natural stream.”

San Jose Penitencia Creek Park Upper Penitencia Creek Trail

• 38 Acres • 3.15 miles from King St to Toyon St • Amenities: youth playground, picnic sites, trail, parking, • Mostly paved Class 1 bike/pedestrian trail restrooms • Operated by City of San Jose (CSJ) Dept. of Neighborhood • Operated by City of San Jose (CSJ) Dept. of Neighborhood Services, Parks, and Recreation Services, Parks, and Recreation • Connects to Many Parks: Penitencia Creek, Commodore, Penitencia Creek County, and Alum Rock Parks

1 Upper Penitencia Creek Trail City of San Jose Overfelt Gardens Park

• 32. 6 acre park with picnic areas and Chinese cultural garden • About 0.5 mile south of Reach 2 of Upper Penitencia Creek • SCVWD provides water for park via Mabury diversion on Upper Penitencia Creek, Mabury Pond and pipeline • Stormwater flows to Miguelita Creek