The upper creek originates in the historic Rancho La Purisima Concepcion, which was granted by Governor Alvarado in 1840 to Jose Gorgonio, an Indian living at Mission Santa Clara.

[11] Designated a California State Historical Landmark in 1954, the 160-year-old Juana Briones home was scheduled for demolition in 2007 because of damage to it by the Loma Prieta earthquake in 1989.

This meant more and more wells, including large ones dug along Adobe Creek by early water companies to serve the little town of Los Altos.

[6] The Trust for Hidden Villa is a nonprofit educational organization founded by Frank and Josephine Duveneck, who purchased most of the land comprising the upper Adobe Creek watershed in 1924.

Over the following decades, the Duvenecks also established the first Hostel on the Pacific Coast (1937), the first multiracial summer camp (1945), and Hidden Villa's Environmental Education Program (1970), all on the creek's upper reaches.

[20] Adobe Creek drains about 11 square miles (28 km2), arising at 2,600 feet (790 m) on the northeastern flank of Black Mountain in Los Altos Hills, California.

A 1919 lawsuit against upstream creek diversion for "alfalfa fields" and "hog wallows" reads: "From time immemorial...the waters of Adobe Creek have flowed into, over upon and through the lands...from Hidden Villa high in the hills, past the wonderful home gardens of Los Altos to the Santa Clara Valley and on to the sea...Charles K. Field mourns the loss of the song of the brook that made his garden with its rockery an enchanted spot; Shoup's children can no longer wade in the stream, because there is no stream to wade in; acres and acres of McCutchen's rhododendrons are now languishing and dying with unsatisfied thirst.

[1] From 2003 to 2009, Upper Reach 5 of Adobe Creek (between Foothill Expressway and West Edith Avenue) was restored in an innovative partnership called the Adobe Creek Watershed Group with representatives from the Santa Clara Valley Water District, local residents and representatives of the City of Los Altos and the Town of Los Altos Hills.

After crossing Foothill Expressway it is buried in an underground pipe just west of Gunn High School but sees daylight where the creek crosses Bol Park Bike Path in a small, man-made flood control basin, then at Laguna Avenue again enters an underground pipe running beneath Los Robles Avenue to El Camino Real.

After passing under Highway 101, Adobe Creek enters the Palo Alto Flood Basin just west of a levee at the end of San Antonio Road.

In the 1800s the Baylands marshes ended between Alma and El Camino Real in Palo Alto, which explains why historical maps show area creeks appearing to terminate before they reach the Bay.

[42] The coast redwoods (Sequoia sempervirens) were transplanted by the Halsey family from a location on Summit Road in the Santa Cruz Mountains and replaced the native willows.

[43] On June 16, 2010, the Los Altos City Council finalized the purchase of 10,000 square feet (930 m2) of creekside property from Delbert and Marlene Beumer, who wanted to provide a safe pathway connecting Shoup Park and Redwood Grove.

[50] Steelhead spawning runs were partially blocked by construction of the tidal gate in the Palo Alto Flood Basin at the mouth of Adobe Creek in 1957.

[22] In 1959, steelhead trout spawning runs were completely blocked by another flood control project on Adobe Creek, when the Santa Clara Valley Water District transformed the natural stream channel into a concrete trapezoidal chute with eight foot drop and dysfunctional fish ladder below El Camino Real.

The 2.4 miles (3.9 km) long concrete trapezoidal channel structure from El Camino Real northward to Highway 101 stops fish with thin sheets of rapid horizontal flow during winter.

Additional barriers occur at the O'Keefe Lane and Hidden Villa bridges, and the creek suffers from significant bank erosion, failing channel stabilization structures, and sedimentation.

[51] Finally, the trash rack at the tidal gate at the mouth of Mayfield Slough in the Palo Alto Flood Basin continues as an intermittent complete barrier to fish passage when it is closed.

[52] Leidy reported the fish still inhabiting the Adobe Creek's lowest reach in 2007 – native California roach, Sacramento sucker, three-spined stickleback, and non-native common carp (Cyprinus carpio), rainwater killifish (Lucania parva), and western mosquitofish (Gambusia affinis).

[53] A 2011 fish survey utilizing electrofishing showed only native fish above El Camino Real: the reach above Redwood Grove and the Manresa Lane bridge in Los Altos included California roach, Sacramento sucker and three-spined stickleback – an assemblage that generally includes steelhead trout in other Bay Area streams.

Further upstream, the diversity of the fish assemblage steadily diminishes due to passage barriers and reduced stream flows from diversions and wells: at Moody Road just above Foothill College, only California roach and three-spined stickleback were collected, at Rhus Ridge bridge in Los Altos Hills only three-spined stickleback were collected, and at the Francemont Avenue bridge and along the Adobe Creek Trail at Hidden Villa no fish were found.

The tidegate consists of several weirs and one operator-controlled sluice gate that enables tidal flows into the basin in order to improve water quality and for mosquito control.

[55] In 2002 a small opening was cut in the trash grate on the tidal gate to permit fish passage but local fisherman in the Flood Basin no longer report catching steelhead trout in recent years.

From November 16 to 20, 2002, approximately 100 striped bass (Morone saxatilis), 5 bat rays (Myliobatis californica) and 2 leopard sharks (Triakis semifasciata) were found dead in the Flood Control Basin in both Adobe and Matadero Creeks within one mile of the tidegate.

This is supported by the fact that the dead fish were all large (requiring more oxygen) at 2 to 4 feet long and the mouths and gills of the bass were fully extended open.

A scenic, easy walking or mountain biking trail, it also provides outstanding birdwatching and in winter is known for its flock of American white pelicans (Pelecanus erythrorhynchos).

The Charleston Slough is a rich salt marsh and littoral zone, providing feeding areas for a variety of shorebirds and other estuarine wildlife.

The sailing station boat launching dock is visible on the opposite shore of the channel at the mouth of the former Palo Alto Yacht Harbor.

Baylands Nature Preserve surrounds what used to be the Palo Alto Yacht Harbor, now a silted-in mud flat and marsh which provides excellent birding.

Hidden Villa is the starting point for the relatively gentle Adobe Creek Trail, an easy two mile hike upstream along a cool, wooded canyon.