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The saratoga creek system

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SFEI, Historical Vegetation and Drainage Patterns of Western Santa Clara Valley, (Historical Conditions Circa 1850).

nATURAL FEATURES AND ECOSYSTEM

San Tomas Aquino Creek

San Tomas Aquino Creek is located along the eastern property line of the Santa Clara Square Apartments. The San Tomas Aquino Creek is also located ~700 feet from The Chip Fab. The Creek originates in the Santa Cruz mountains and flows into the valley floor. Historically the Creek does not appear to have extended to the SF Bay.

The Creek is exposed with moving surface water; thus, air pollution can easily settle in the water and on the banks of the creek. The Creek flows north out to Guadalupe Slough, into the SF Bay, and into the Pacific Ocean. The bottom of San Tomas Aquino Creek has an elevation of 15.5 feet to 19.6 feet.” (Geotechnical Investigation, Santa Clara Square, pg6, 24 July 2015; SCSA Hydrology Study ,August 17, 2015).

“The creek has been heavily altered from its natural state…  bound by paved and concrete reinforced levies on both banks…. channelized and altered from its native state.” (SCSA Biological Resources Assessment, 2015). The “Santa Clara Square Biological Resources Assessment” noted in passing that San Tomas Aquino Creek might be “potentially within the jurisdiction of USACE under Section 404 of the Clean Water Act” (May 2015).

Prior to artificial modifications, San Tomas Aquino Creek channel lost its definition well before reaching the SF Bay and was notably shallow and poorly defined (Beller, E. et al, Nov. 2010). Survey notes described the creek as "very shallow" and about four meters wide (Beller, E. et al, Nov. 2010).

The natural flow of San Tomas Aquino Creek displayed characteristic serpentine terrane behavior. Reports described the "scatters" of the creek around Hamilton Avenue, and the "sink" of the creek around Williams Road, a mile further north (Beller, E. et al, Nov. 2010). One early map shows two termini of the creek labeled "sink of creek". These descriptions illustrate the shallow, discontinuous nature of the channel, which presumably spread into a marsh and disappeared into coarse gravels. Disconnected distributary channels then rose from pressurized aquifers and flowed north below the terminus of the superficial waters of the San Tomas Aquino Creek, hydrologically connecting to Sanjon Creek and the SF Bay.
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Serpentine forms when oceanic crust are altered by hydrothermal fluids and it creates highly fractured, permeable bedrock with extensive underground flow networks. The Creek’s hydrological behavior reflects natural fracture systems through serpentinized basements. The Creek is following natural fracture systems through the serpentine bedrock, which is why it "scatters," develops multiple "sinks," and loses its defined channel before reaching the Bay.

Despite modern alterations, the San Tomas Aquino Creek still supports native plant and fish species and is considered a sensitive biological community. The formal “Beneficial Uses” of the San Tomas Aquino Creek include “freshwater replenishment, ground water recharge, cold freshwater habitat, fish migration, preservation, and spawning, warm freshwater habitat, wildlife habitat, and recreation” (RWQCB, SFB, 2009).

San Tomas Aquinas Creek  is managed under Clean Water Act 303(d). (EPA Id. CAR2055004020080624165713). The formal TMDL pollutants are “trash.”

Recent sightings reported to iNaturalist in 2024 confirmed the continued presence of fish in the creek near the Santa Clara Square Apartments and Chip Fab, including Chinook Salmon (Oncorhynchus tshawytscha) (Nov 12-13 2024, iNaturalist, Id. No. 251599313, 251464788) and European Carp (Cyprinus carpio) (March 2024, iNaturalist, Id. No. 216635588) in San Tomas Aquino Creek.

The Saratoga Creek

Saratoga Creek is a tributary that originates from the Santa Cruz Mountains around Castle Rock Ridge. It has also been named Arroyo Quito, Campbell Creek, Big Moody Creek, and San Jon Creek where it flowed to the Sloughs and Bay.

Saratoga Creek is ancient and was one of the sources of the sedimentary deposit of "alluvial fans" of the valley floor. (Cal. Dept. of Consv. 2002). The Creek “once surged with mountain runoff.”  Academic reconstruction of historic Bay Area ecology and watersheds (1800-1850) document Saratoga Creek as the only permanent creek in the Santa Clara County area that flowed from the Santa Cruz mountains to the Bay (alongside the Guadalupe River).

Saratoga Creek flowed from the hills in southern Saratoga, alongside ponds and marshes, and repeatedly sunk and reemerged through the valley floor. Saratoga Creek consolidated into the Sanjon Creek past what is now US 101, where the Creeks transition into a “wet meadow” with salt marshes, and eventually flowed with the Guadalupe River at the San Francisco Bay tidal marshlands and flowed out into the Pacific Ocean. (SFEI, 2010). 

In northern Santa Clara, after the transition boundary where Sanjon and Saratoga Creeks became wet meadows, but before they transitioned to marshland, there were also unique “alkali meadows" that supported rare and specialized alkaline ecosystems (Beller et al., 2010; Reed, 1862). Serpentine soils are known for hosting rare and endemic plant species because few plants can tolerate the high mineral content and low nutrient levels, such as in “alkali meadows.” 

The locations where the historic Saratoga Creek would sink and disappear, only to rise up again and still find its way to connect to Sanjon, the marshlands, and the Bay, are regions of Santa Clara near assumed concealed faults and unexplained magnetic anomalies (Chase, 1992; Schmidt et al., 2014). These areas of Santa Clara that appear to have unmapped faults, are also thought to contain “major serpentine sheet,” based on aeromagnetic anomaly data (Roberts and Jachens, 2003; Wentworth, 2010). 

Major, historic earthquakes caused targeted, fault-like patterns of property damage in Santa Clara, despite the City of Santa Clara having not known or mapped faults – and similar damage only occurring in areas around established faults. The nearest mapped fault is Monte Vista-Shannon, which is about 12km southwest of The Premise. 

The fault at Monte Vista-Shannon is also where the Saratoga and San Tomas Aquino Creeks enter the valley from the hills. If Saratoga Creek/aquifer flowed through the valley floor, both on the surface and also deep within hydrothermal systems, it would be expected the flow of the creek/aquifer followed the location and direction of a series of mini faults along the valley floor and traveling to the Bay, which would charge the aquifer. 

San Tomas Aquino Creek was “channelized” around 1965. (EKI, SCS, 2013). Then, Saratoga Creek was “filled” at some point around 1970-1974 (Freedom Circle ESA, 1997). By 1974, Saratoga Creek was filled and “the area where the creek ran has been graded” and an industrial office park was built on the filled land by 1976. (EKI, SCS, 2013). Saratoga Creek surface waters historically flowed across what is currently known as 3260 Scott Blvd and 3250 Scott Blvd (between the two buildings), across Montgomery Drive along the Santa Clara Square Apartments. 

Saratoga Creek is managed under Clean Water Act 303(d). (EPA Id. CAR2055004019990218133956). The formal TMDL pollutants are “trash” and Diazinon. Saratoga Creek and San Tomas Creek are “major drainages that pass through Santa Clara Valley” and “originate in the Santa Cruz Mountains.” (Santa Clara Valley Habitat Plan, Ch. 3, Pg. 8, Aug. 2012). 

The current confined, subterranean aquifer located under, and sometimes bubbling out onto, The Premise – is located squarely within this zone of apparent serpentine hydrothermal systems, including earthquake damage from assumed concealed faults and the unusual alkaline ecosystems. It also located just south of the nexus for the alkali wetlands and meadows (estimated to be located between Lawrence Expressway and San Tomas Expressway (W-E), and Bayshore Freeway/U.S. 101 and Central Expressway(N-S)).

The Underground Aquifer System 

The entire Saratoga Creek system—including the artesian springs, the creek (both above ground and where it flows deep into the serpentine before resurfacing), the alkali meadows and sloughs connected to the bay and ocean—are all likely part of the "waters of the US" and subject to  Clean Water Act regulation. Saratoga Creek is definitely regulated under CWA because it is a tributary to the bay and ocean. But the entire Saratoga Creek system has a clear, continuous hydrological connection via the creek, sloughs, and bay, to a traditional navigable water with the ocean/bay. The alkali meadow and sloughs had (and could have again) hydrophytic vegetation, hydric soils, and wetland hydrology – all of which is adjacent to the creek and the bay/ocean.

The evidence strongly implies that the Saratoga Creek system’s continuous and consistent flow arises from a hydrothermal system which is at least as a "relatively permanent" water body. The specific point where the water comes back up from the hydrothermal system is part of the continuous flow path of the jurisdictional creek. United States v. Moses, 496 F.3d 984 (9th Cir. 2007) - buried creek in culvert still "waters of the US" . Headwaters, Inc. v. Talent Irrigation Dist., 243 F.3d 526 (9th Cir. 2001) - underground flow does not remove jurisdiction.

There are multiple lines of evidence suggesting that the Saratoga Creek system is still flowing underground in/around the historic location of the Creek. One of the most compelling data sources is the presence of multiple, documented natural springs and “artesian features” on The Premise. (See Figure 1, created by the Plaintiff).

Saratoga Creek originates from areas of Santa Clara Vally that are famous for natural springs, serpentine, and hydrothermal systems (Congress Springs, etc.). Historic aerial photos of the Premise show Saratoga Creek as a consistently flowing Creek. Seasonal serpentine seeps appear like grasslands in winter months, but all photos of the Premise show a consistently flowing Creek.
92. USGS has mapped ninety-two springs across Santa Clara Valley and only seven active springs occur on serpentine soils. These springs may provide “serpentine seeps” which provide critical habits for alkaline/serpentine-associated species like Mt. Hamilton thistle.” (Santa Clara Valley Habitat Plan, Ch. 3, Pg. 8, Aug. 2012). 

Seeps occur when water penetrates the surface and creates a small wetland habitat that supports wetland vegetation. Serpentine seeps are a “Sensitive Land Cover Type” and the “equivalent to sensitive natural communities as defined by the California Department of Fish and Game.”  “Serpentine seeps are a type of wetland and… alteration of hydrologic regimes by adjacent land uses and development can change and, in some case, remove the water source for these seeps. This can result in partial or complete loss of seep wetlands.” (Santa Clara Valley Habitat Plan)

Here, at The Premise, we now have at least six natural springs documented at the Premise following penetrations into the ground and groundwater systems. Two are at the Synertek site, and five are at the Santa Clara Square Apartments.

These springs were discovered by multiple environmental contractors, with some monitored for decades, and the data was consistent with an interconnected underground, flowing aquifer. However, the springs all represent the same deep, alkali water system – with unexpected pressure and force – and the surrounding soils all show extensive evidence of serpentine.

At the Synertek site (3050 Coronado Dr.), Honeywell groundwater monitoring well MW-03B1 is frequently mentioned in federal and state monitoring reports (i.e., it “has historically been observed to be an artesian well based on water seen on the pavement around the well and the depth to water measured as the top of casing” -- Synertek GW January 28, 2015).  

The well was dug around 1988 to monitor the B1 aquifer and only allows inflow of water from 100-105 ft below ground (CH2MHill, Synertek, 2010). For the last thirty-years, well MW-03B1 has been documented to release water from deep underground aquifers, contained under such pressure that the water naturally rises one hundred feet up the well shaft, and continues to rise, spilling out onto the pavement. However, when the well was dug in 1988 the water level was nineteen feet below surface, and then as the pressure increased the depth to water decreased, hitting zero feet below surface in 1995 and remaining there in subsequent annual measurements. (CH2MHill, Synertek, 2010). The pH of water from well 3B1 generally trends to alkaline. 

A second Honeywell B1 aquifer ground monitoring well at the Synertek site, (MW-20B), also taps into a pressurized source with increasing pressure raising the water level starting from in 2001. The MW-20B well allows inflow of water from 34-44 feet below the surface, and the pressured water rises up to at or near the surface. 

The pressure measured in MW-20B places its surface level (how high it wants to rise above its water level) at around thirty-five feet with a depth to water of 0 in 2010. (CH2MHill, Synertek, 2010). Water tested from MW-20B is alkaline and with pH values greater than nine, and in 2012 the pH even exceeded 11 (the pH of ammonia).

The groundwater reports note there are “variations in vertical hydraulic gradient” and the pressurized flow at MW-03B1 and MW-20B represent “localized hydraulic mounds.” (CH2MHill, Synertek, 2010). The excavated soil for 3B1 was olive grey, dark grey, grayish green to dark green, and olive to olive grey. (Geotracker). The excavated soil for MW-20B was colored dark olive, pale olive, olive and wet, olive-grey, olive brown, dark grey, and “mottled rust.” The gradients and  soil coloring provides additional evidence to support that this aquifer and the springs are part of a serpentine hydrothermal system. 

In 2015, the EIR for the Santa Clara Square Apartments noted a large, pressurized, underground aquifer (which they referred to as an “artesian feature”) flowing only ~35 feet beneath the surface and across a distance of at least three blocks wide. (Santa Clara Square Apartments, EIR, Oct. 2015). Two of the springs (C6-3 & C5-2) had water flowing up and out of the ground (Geotechnical Investigation, Santa Clara Square, 24 July 2015). 

Groundwater Well C6-3 appears to be located in Creekside Park at the SW corner of the apartments and adjacent to The Chip Fab. In addition, a 2015 boring hole at around 15 ft deep, south of Creekside Park, was noted as “very moist – boring may fill with water by tomorrow.” (Cal. EPA DTSC, Santa Clara Square Apartments, 2015). Well C5-2 is located around Scott Blvd and Montgomery Drive, along the original Saratoga Creek bed, and north of The Chip Fab.

The Geotechnical Report explained that wells were dug for Cone Penetration Tests and four of those wells were pressured springs (“artesian features”) contained by a 5-10 foot layer of “sand and gravel” and “silty to sandy clays” at around thirty-five feet below the surface. The pressure measurements for all four springs estimated that a natural flow under current conditions would result in the water spitting up to 10 to 13 feet in the air and above the surface. (Geotechnical Investigation, Santa Clara Square, 24 July 2015).

Project reports also noted the elevation of groundwater at the Premise seem to fluctuate in relation to the ground-level flow of the San Tomas Aquino Creek, indicating the underground Saratoga Creek aquifer and the ‘channelized” San Tomas Aquino Creek are receiving water from the same/similar locations to the south. 

The EIR for Santa Clara Square Apartments addressed what appears to an expansive, flowing, active underground aquifer – representing the deeper levels of the “filled” Saratoga Creek -- by simply stating that Saratoga Creek was “filled” in 1968-1980. And “if  excavations are not made into the sand and gravel layer approximately thirty-five feet bgs… the artesian condition should not affect the project.” (Geotechnical Investigation, Santa Clara Square, p. 16, 24 July 2015). 
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offical Maps & aerial photographs

1800s
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1930s
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Aerial Photograph, Scale: 1"=500', Flight Year: 1939, Source: Fairchild
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Aerial Photograph. Scale: 1"=500' Flight Year: 1939 USGS
1940s
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Aerial Photograph, Scale: 1"=500', Flight Year: 1948, Source: USGS
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Aerial Photograph. Scale: 1"=500' Flight Year: 1948 USGS
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Aerial, 1948, 229 mm x 299 mm, 152.31 mm
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Aerial, 1948, 229 mm x 299 mm, 152.31 mm
1950s
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Aerial Photograph. Scale: 1"=500', Flight Year: 1956, Source: Aero
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Aerial Photograph. Scale: 1"=500' Flight Year: 1950 USGS
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Aerial Photograph. Scale: 1"=500' Flight Year: 1956 USGS
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1960s
​​Santa Clara Valley Water District, A model study of the hydraulic structures at the confluence of the San Tomas Aquino and Saratoga Creeks, (1965).
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Aerial, Aug. 15 1960
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Aerial, Aug. 15 1960
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Aerial Photograph. Scale: 1"=500' Flight Year: 1968 USGS
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Aerial Photograph. Scale: 1"=500' Flight Year: 1968 USGS
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Aerial, Oct 1 1968, 457 mm x 229 mm
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Aerial, Oct 1 1968, 457 mm x 229 mm
1970-1973
Santa Clara Valley Water District, Report on condition and status of Saratoga Creek within the Santa Clara City limits (San Tomas [Aquino] Creek confluence to Stevens Creek Boulevard), (1973).

 Santa Clara Valley Water District, Ecological report: Saratoga Creek (1973).
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1970, California EPA, RWQCB Notes (GeoTracker)
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Aerial, May 1972
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Aerial, April 29 1970, 457mm x 229 mm, 65,000 ft, 608 mm
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Aerial, April 29 1970, 457mm x 229 mm, 65,000 ft, 608 mm
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Aerial, July 27 1972
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Aerial, July 27 1972, zoomed
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Aerial, May 22 1972, 23,013 ft
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Aerial, May 1972
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Aerial, Dec. 13 1972, 65k ft
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Aerial, Dec. 13 1972, 65k ft
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Aerial, March 23 1973, 65K Ft
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Aerial, March 23 1973, 65K Ft
1974-1976
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Aerial, June 6, 1974, 10k Ft
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Aerial Photograph. Scale: 1"=500' Flight Year: 1974 USGS
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Aerial Photograph. Scale: 1"=500' Flight Year: 1974 USGS
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Aerial, Sept. 1974
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Aerial, Feb 1974
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Aerial, July 25 1974, 457 mm x 299 mm, 913 mm
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Aerial, June 6 1974
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1977-1979
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Saratoga Creek Drainage Area (1978)
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San Tomas Aquino Creek Drainage Area (1978)
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Aerial, 1977
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Aerial Photograph. Scale: 1"=500' Flight Year: 1979 USGS
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1980s
Santa Clara Valley Water District, San Tomas Aquino/Saratoga Creek Planning Study: Summary Report (1981).
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1983
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1983
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Aerial, 1989
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1982 Aerial Photograph. Scale: 1"=500' Flight Year: 1982 USGS
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Aerial Photograph. Scale: 1"=500' Flight Year: 1982, Source: WSA
1990s
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Aerial Photograph. Scale: 1"=500', Composite DOQQ - acquisition dates: 1993, Source: EDR
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Aerial Photograph. Scale: 1"=500' /DOQQ - acquisition dates: 1993 USGS/DOQQ
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Aerial, NAPP, 1993
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1992
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1992
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1994
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Aerial, NAPP, 1993
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Aerial Photograph. Scale: 1"=500' Flight Year: 1998 USGS Best Copy Available from original source
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Aerial Photograph. Scale: 1"=500' Flight Year: 1999, Source: WAC
2000s
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Aerial Photograph. Scale: 1"=500' Flight Year: 2005 EDR
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Aerial Photograph, NAIP, 2005
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Aerial Photograph. Scale: 1"=500' Flight Year: 2005 USDA/NAIP
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Aerial Photograph. Scale: 1"=500' Flight Year: 2006 USDA/NAIP
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2009 Aerial Photograph. Scale: 1"=500' Flight Year: 2009 USDA/NAIP
2010s
Santa Clara Valley Water District, Saratoga Creek hazard tree removal and restoration project: Final initial study and mitigated negative declaration (2019).
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Aerial Photograph. Scale: 1"=500' Flight Year: 2010 EDR
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Aerial Photograph. Scale: 1"=500' Flight Year: 2012 EDR
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Aerial, 2018, USDA/FSA APFO CNIR
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Aerial, 2022, USDA/FSA APFO CNIR

natural ecosystem

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hsbay150p4_opt.pdf
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Reports & Technical Articles: 
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Beller, EE; Salomon, M; Grossinger, RM. 2010. Historical Vegetation and Drainage Patterns of Western Santa Clara Valley: A technical memorandum describing landscape ecology in Lower Peninsula, West Valley, and Guadalupe Watershed Management Areas. SFEI Contribution No. 622. SFEI: Oakland. 
historicalecology_of_western_santaclaravalley_sfei_111910.pdf
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County of Santa Clara, Historic Context Statement, Department of Planning and Development Planning Office, (December 2004, Revised February 2012).
hhp_201202_historic_context.pdf
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Grossinger, RM; Striplen, CJ; Askevold, RA; Brewster, E; Beller, EE. 2007. Historical landscape ecology of an urbanized California valley: wetlands and woodlands in the Santa Clara Valley. Landscape Ecology 103-120.
hep_landscape_ecology_2007.pdf
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​Lowe, S; Salomon, M; Pearce, SA; Collins, JN; Titus, D. 2019. West Valley Watershed Assessment 2018: Baseline Ecological Condition Assessment of Southwest San Francisco Bay Creeks in Santa Clara County; Calabazas, San Tomas Aquino, Saratoga, Sunnyvale East and West. SFEI Contribution No. 944. San Francisco Estuary Institute: Richmond.

​Lowe, S; Salomon, M; Pearce, SA; Collins, JN; Titus, D. 2018. 
West Valley Watershed Assessment 2018: Study Area Extent, Stream Survey Design, Sample Frame, and Sample Draw. SFEI Contribution No. 863. San Francisco Estuary Institute: Richmond, CA.
westvalley_watershedconditionmemo_20190520_final.pdf
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Lowe, S; Pearce, SA; Salomon, M; Collins, JN; Titus, D. 2020. Santa Clara County Five Watersheds Assessment: A Synthesis of Ecological Data Collection and Analysis Conducted by Valley Water. SFEI Contribution No. 963. San Francisco Estuary Institute: Richmond, CA.

Mallen, Claire, "Assessing Methods for Determining Reference Conditions for Riparian Restoration in Santa Clara County" (2020). Master's Theses. 1448. https://repository.usfca.edu/thes/1448

Berkley, SF Bay Delta (2004).

Odell, J, Excavating Calabazas Creek: An Inefficient Route Through Silicon Valley​​ (2019).

Guidance Documents:

Hagerty, S; Spotswood, E; McKnight, K; Grossinger, RM. 2019. Urban Ecological Planning Guide for Santa Clara Valley. SFEI Contribution No. 941. (See also, Resilient Silicon Valley).
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SFEI, Urban Ecological Planning Guide for Santa Clara Valley.
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SFEI, Urban Ecological Planning Guide for Santa Clara Valley.

GIS Data & Mapping:

Sowers, JM; Salomon, M .N.; Ticci, M; Beller, EE; Grossinger, RM. 2012. Watching Our Watersheds: Santa Clara Valley Past, Google Earth KMZ files: Santa Clara Valley historical points of interest, stream courses and habitats.

EcoAtlas, Historical Aquatic Resources and Terrestrial Plant Communities, California Bay Area 

SFEI: Santa Clara Valley historical ecology GIS
​SFEI: Western Santa Clara Valley Historical Ecology Study

Santa Clara Valley Hydrology

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SFEI, Historical Vegetation and Drainage Patterns of Western Santa Clara Valley, (Historic 1800 v Modern 2007 Drainage)
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Resources

Barnes I, Lamarche VC Jr, Himmelberg G. Geochemical evidence of present-day serpentinization. Science. 1967; 156 (3776): 830-832. doi:10.1126/science.156.3776.830

Ultrabasic (pH > 11) water issues from some fresh ultramafic bodies. The properties of the ultrabasic solutions are believed to be due to current reactions yielding serpentine from primary olivines and pyroxenes. The low concentrations of divalent airon. divalent magnesium, and dissolved silica from the serpentinization require an increase in rock volume.
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RH Whitaker, Ecology of Serpentine Soils, Ecology, Volume 35, Issue 2 (April 1954), 258-288.

Melosh, B. L. (2019). Fault initiation in serpentinite. Geochemistry, Geophysics, Geosystems, 20, 2626–2646. https://doi.org/10.1029/2018GC008092

CGS NOTE 57: SERPENTINITE AND SERPENTINE IN CALIFORNIA, California Dept. of Conservation

Klein, F., Goldsby, D. L., Lin, J., & Andreani, M. (2022). Carbonation of serpentinite in creeping faults of California. Geophysical Research Letters, 49, e2022GL099185. https://doi.org/10.1029/2022GL099185

Brady, Kruckeberg, Bradshaw Jr, EVOLUTIONARY ECOLOGY OF PLANT ADAPTATION TO SERPENTINE SOILS, Annu. Rev. Ecol. Evol. Syst. 2005. 36:243–66 (2005)

Oze, Christopher & Skinner, Catherine & Schroth, Andrew & Coleman, Robert. (2008). Growing up green on serpentine soils: Biogeochemistry of serpentine vegetation in the Central Coast Range of California. Applied Geochemistry - APPL GEOCHEM. 23. 3391-3403. 10.1016/j.apgeochem.2008.07.014.

DONALD E WHITE; THERMAL WATERS OF VOLCANIC ORIGIN. GSA Bulletin 1957; 68 (12): 1637–1658. doi: https://doi.org/10.1130/0016-7606(1957)68[1637:TWOVO]2.0.CO;2
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