Alameda Creek historically supported spawning runs of at least three salmonid species:
steelhead (the
anadromous form of the coastal rainbow trout
Oncorhynchus mykiss irideus),
coho salmon (
Oncorhynchus kisutch) and
Chinook salmon (
Oncorhynchus tshawytscha). The last steelhead and coho salmon runs in the 20th century were seen in the lower creek in 1964, the latter confirmed by photographic records. In 2009, the
Alameda County Water District removed a rubber dam that blocked trout passage in the lower creek, adjacent to
Quarry Lakes Regional Park. In June, 2010 environmentalists and water district officials celebrated the removal of a dam on Alameda Creek in Fremont, and the planned installation of fish ladders to allow salmonids to bypass two other dams on the lower creek. At the same time,
PG&E worked to modify a cement barrier farther upstream in
Sunol to help steelhead swim farther into the watershed, water officials said. Ground was broken on the first ladder the
Alameda County Water District was building in April 2018, just west of the Mission Boulevard overcrossing in the Niles district of Fremont, allowing passage around a rubber dam. The second ladder, which was planned to start construction in 2019, is about a mile downstream at the concrete structure, called a
weir. The two ladders were funded by nearly $10 million in grants from several agencies, including $5.36 million from the California Wildlife Conservation Board and $3 million from the California Natural Resources Agency. The goal was that when those projects were completed in 2021, steelhead would be able to migrate upstream to spawning habitats in the Sunol Valley for the first time in a half-century. The following year, monitoring by the
San Francisco Public Utilities Commission recorded 50 tagged steelhead making the migration up Alameda Creek to the San Francisco Bay.
Other fish California's archaeological record has contributed to knowledge of the prehistoric distribution of fishes in Alameda Creek and its tributaries including
Sacramento perch (
Archoplites interruptus), Sacramento suckers (
Catostomus occidentalis occidentalis),
Tule perch (
Hysterocarpus traskii),
Hitches (
Lavinia exilicauda),
Hardheads (
Mylopharodon conocephalus),
Sacramento blackfish, and Sacramento pikeminnow (
Ptychocheilus grandis). Recent physical evidence has proved that the southern limit of coastal Chinook salmon included the southernmost tributaries of South San Francisco Bay. Many of these fishes still occupy the creek. In 2023, a likely new species of
lamprey (
Lampetra sp.) was discovered in Alameda Creek by
mitochondrial DNA genetic testing. The number of introduced exotic fishes continues to increase in Alameda Creek and other San Francisco Bay tributaries with man-made reservoirs. Exotic fish species such as the
largemouth and
smallmouth basses (
Micropterus salmoides and
Micropterus dolomieui) respectively, were introduced to Alameda Creek (and the
Napa River) by Livingston Stone in 1874.
Beaver There is historical evidence of
beaver in the Alameda Creek watershed. In 1828 fur trapper
Michel Laframboise travelled to "the missions of
San José,
San Francisco Solano and
San Rafael Arcángel. La Framboise stated that "the Bay of San Francisco abounds in beaver", and that he "made his best hunt in the vicinity of the missions".
Alexander Roderick McLeod reported 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". In the 1840s
Kit Carson was granted rights to trap beaver on Alameda Creek in the East Bay where they "abounded...from the mouth of its canyon to the broad delta on the bay". Physical evidence of beaver include
faunal remains in the
Arroyo de la Laguna tributary recovered in an archaeological site west of
Interstate 680. Beaver may be beneficial to efforts to restore salmonids in Alameda Creek as beaver ponds benefit oversummering salmonid smolts by raising the water table which then recharges streams in the dry summer season and also by providing perennial deep pools when streams are only seasonal. ==Conservation==