The river's Los Alamitos and Guadalupe Creek tributaries are, in turn, fed by smaller streams flowing from Almaden Quicksilver County Park, home to former mercury mines dating back to when the area was governed by Mexico.

[5] The historic de Anza Expedition explored much of Santa Clara County, traversing western areas en route from Monterey to San Francisco, and traveling around the south end of San Francisco Bay and thence through the eastern portions of the county on the return trip after exploration of parts of the East Bay.

[7] On July 9, 2005, the fossilized bones of a juvenile Columbian mammoth were discovered by San Jose resident Roger Castillo in the Lower Guadalupe River near the Trimble Road overcrossing.

[16] The SCVWD manages water flows (supply) and provides flood control on the river, and recently has started to promote watershed stewardship.

Ending nine years of study and passionate debate about the future of the San Jose/Alviso waterfront, the Santa Clara Valley Water District in November, 2009 voted to approve a $6 million project to clear bulrushes, tule reeds and thick sediment from the Guadalupe River in Alviso.

[18] A recent ancient DNA sequencing study of salmonid remains excavated from Mission Santa Clara dating to 1781–1834 CE found that of 58 salmonid vertebrae analyzed, three samples had DNA sequences indicating Chinook salmon (Oncorhynchus tshawytscha), the other 55 were steelhead trout (Oncorhynchus mykiss).

Chinook salmon were historically abundant in the Sacramento River and would pass through San Francisco Bay to marine habitats, but rarely entered streams south of San Francisco Bay,[20] and were not documented in the Guadalupe River watershed or other Santa Clara County streams prior to the 1980s.

Both steelhead trout, which were recorded in select Santa Clara County streams historically, and Chinook salmon runs occur in the Guadalupe River watershed today when conditions are appropriate.

In 2012, the Santa Clara Valley Habitat Plan reported that Chinook salmon currently spawn in the Guadalupe River and its tributaries, as well as Coyote Creek.

[24] On the Los Gatos Creek tributary a population of California Golden beavers (Castor canadensis subauratus) has been re-established between Lake Elsman and Lexington Reservoir.

[25] Video documentary by Greg Kerekes documented beaver in the Guadalupe River mainstem in downtown San Jose in April, 2013.

According to scientists from the U.S. Geological Survey, Caspian tern populations in the South Bay are declining at the same time that high levels of mercury are being found in their eggs.

The highest mercury levels found in animals from the Bay were in the eggs of Caspian and Forster's (Sterna forsteri) terns that nest near the Cargill salt ponds at the mouth of the Guadalupe River.

After four years of the harsh California drought, in July 2015, the river ran dry for an 8-mile stretch through the city of San Jose.

This was due to inadequate storage in upstream reservoirs for the releases of water needed to sustain flow to the river mouth until winter rains returned.

An estimated 6,500 tons of mercury was lost in the system of creeks and rivers along the coast between 1850 and 1920, and is currently being detected today in the local streams, animal life, and riverbeds of these affected tributaries.