The Sacramento River and its drainage basin once supported extensive riparian habitat and marshes, in both the Sacramento Valley and the Delta, home to a diverse array of flora and fauna.
Due to the reclamation of land for agriculture and the regulation of seasonal flooding, the amount of water-based habitat declined greatly during the 20th century.
Other human impacts include the heavy water consumption for agriculture and urban areas, and pollution caused by pesticides, nitrates, mine tailings, acid mine drainage and urban runoff.
The Sacramento supports 40–60 species of fish, and 218 species of birds.
The basin also has a number of endemic amphibian and fish species.
Many Sacramento River fish species are similar to those in the Snake–Columbia River systems; geologic evidence indicates that the two were connected by a series of wetlands and channels about 4-5 million years ago.

Located along the Pacific Flyway, the sprawling wetlands of the Sacramento Valley are an important stop for migratory birds; however, only a fraction of the historic wetlands remain.
Seasonally flooded rice paddies in the Sacramento Valley comprise a large portion of the habitat currently used by migrating birds.
Native bird populations have been declining steadily since the 19th century.
Species that were once common but now are endangered or gone include the southwestern willow flycatcher, western yellow-billed cuckoo, least Bell's vireo, and warbling vireo.
Another reason for dropping numbers are the introduction of non-native species, such as the "parasitic" cowbird, which lays its eggs in the nests of other bird species causing its hatchlings to compete with the others for food.

There were once 9 species of amphibians that used the Sacramento River, but some have become extinct and most other populations are declining due to habitat loss caused by agriculture and urban development.
Amphibians originally thrived in the marshes, sloughs, side-channels and oxbow lakes because of their warmer water, abundance of vegetation and nutrients, lower predator populations and slower current.
This population once included several species of frogs and salamanders; the foothill yellow-legged frog and western spadefoot are listed as endangered species.

Riparian and wetlands areas along the Sacramento once totaled more than 500,000 acres (2,000 km²); today only about 10,000 acres (40 km²) remains.
Much of this consists of restored stretches and artificially constructed wetlands.
Levee construction has prevented the river from changing course during winter and spring floods, which was crucial to the renewal of existing wetlands and the creation of new ones.
Since the late 19th century the river has been mostly locked in a fixed channel, which once could shift hundreds of feet or even several miles in a year because of floods.
In 2010, about 100 miles (160 km) of the river's riparian forests are undergoing active restoration.
The Sacramento River and its drainage basin once supported extensive riparian habitat and marshes, in both the Sacramento Valley and the Delta, home to a diverse array of flora and fauna. Due to the reclamation of land for agriculture and the regulation of seasonal flooding, the amount of water-based habitat declined greatly during the 20th century. Other human impacts include the heavy water consumption for agriculture and urban areas, and pollution caused by pesticides, nitrates, mine tailings, acid mine drainage and urban runoff. The Sacramento supports 40–60 species of fish, and 218 species of birds. The basin also has a number of endemic amphibian and fish species. Many Sacramento River fish species are similar to those in the Snake–Columbia River systems; geologic evidence indicates that the two were connected by a series of wetlands and channels about 4-5 million years ago.
Located along the Pacific Flyway, the sprawling wetlands of the Sacramento Valley are an important stop for migratory birds; however, only a fraction of the historic wetlands remain. Seasonally flooded rice paddies in the Sacramento Valley comprise a large portion of the habitat currently used by migrating birds. Native bird populations have been declining steadily since the 19th century. Species that were once common but now are endangered or gone include the southwestern willow flycatcher, western yellow-billed cuckoo, least Bell's vireo, and warbling vireo. Another reason for dropping numbers are the introduction of non-native species, such as the "parasitic" cowbird, which lays its eggs in the nests of other bird species causing its hatchlings to compete with the others for food.
There were once 9 species of amphibians that used the Sacramento River, but some have become extinct and most other populations are declining due to habitat loss caused by agriculture and urban development. Amphibians originally thrived in the marshes, sloughs, side-channels and oxbow lakes because of their warmer water, abundance of vegetation and nutrients, lower predator populations and slower current. This population once included several species of frogs and salamanders; the foothill yellow-legged frog and western spadefoot are listed as endangered species.
Riparian and wetlands areas along the Sacramento once totaled more than 500,000 acres (2,000 km²); today only about 10,000 acres (40 km²) remains. Much of this consists of restored stretches and artificially constructed wetlands. Levee construction has prevented the river from changing course during winter and spring floods, which was crucial to the renewal of existing wetlands and the creation of new ones. Since the late 19th century the river has been mostly locked in a fixed channel, which once could shift hundreds of feet or even several miles in a year because of floods. In 2010, about 100 miles (160 km) of the river's riparian forests are undergoing active restoration.
Sacramento River