In 1983, torrential rains caused by el Niño resulted in significant flooding of Coyote Creek in the Alviso neighborhood.

On February 24, 2020, the Federal Energy Regulatory Commission ordered that Anderson Lake should be drained due to earthquake risk.

By 4 p.m. February 20, 2017, San Jose City opened an overnight shelter for residents who chose to voluntarily evacuate their homes in low-lying areas along Coyote Creek.

[27] Coyote Creek has historically, and still does support the most diverse fish fauna among the Santa Clara Valley Basin watersheds.

Species known to occur currently include Pacific lamprey (Lampetra tridentata), steelhead/resident rainbow trout (Oncorhynchus mykiss), chinook salmon (Oncorhynchus tshawytscha), California roach, Hitch (Lavinia exilicauda), Sacramento blackfish (Orthodon microlepidotus), Sacramento pikeminnow, Sacramento sucker, three-spined stickleback, prickly sculpin (Cottus asper), riffle sculpin (Cottus gulosus), staghorn sculpin, and tule perch (Hysterocarpus traskii).

[13] 1962 report indicated that Coyote Creek, from its mouth to the headwaters in Henry Coe State Park, was an historical migration route for steelhead trout.

[28] The on-channel percolation ponds constructed on Coyote Creek severely degrade steelhead habitat by harboring non-native fish predators, such as largemouth bass (Micropterus salmoides) which prey on salmonid fingerlings, and also by releasing warm water flows.

Since Chinook salmon spawn in early winter and juveniles migrate to the ocean in their first spring, they are able to use habitats that turn very warm or have low water quality in summer.

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

[31] San Felipe Creek currently contains habitat potentially suitable to coho salmon with low stream temperatures related to cool groundwater discharges in the Calaveras Fault zone.

[32] During early June and late-July 1997, the senior author recorded water temperatures within the San Felipe Creek watershed within pools containing rainbow trout between 51.8 to 55.9 °F (11 to 13.3 °C) and 57.9 to 63.9 °F (14.4 to 17.7 °C), respectively.

[31] A 1962 California Department of Fish and Wildlife report indicates that North American beaver (Castor canadensis) lived in Coyote Creek historically.

[33] This report is consistent with Alexander McLeod's report on the progress of the first Hudson's Bay Company fur brigade sent to California in 1829, "Beaver is become an article of traffic on the Coast as at the Mission of St. Joseph alone upwards of Fifteen hundred Beaver Skins were collected from the natives at a trifling value and sold to Ships at 3 Dollars".

[34] Physical proof of historical beaver in south San Francisco Bay tributaries is a Castor canadensis subauratus skull in the Smithsonian Institution National Museum of Natural History collected by zoologist James Graham Cooper in Santa Clara, California on Dec. 31, 1855.

In late 2023, a Chinook salmon hen was photographed building a redd just below a beaver dam above Charcot Avenue in San Jose (see Photo Gallery below).