Once, profuse runs of anadromous fish—salmon, steelhead, and others—migrated up the Sacramento and San Joaquin Rivers to spawn in great numbers.
The construction of CVP dams on the two rivers and many of their major tributaries—namely Friant Dam and Shasta Dam—mostly ended the once-bountiful Central Valley salmon run.
From north to south, the Sacramento upriver of Shasta Dam, the American upriver of Folsom Dam, the Stanislaus upriver of New Melones Dam, and the San Joaquin upriver of Mendota—have become inaccessible to migrating salmon.
In three of these cases, it is because the dams are too high and their reservoirs too large for fish to bypass via fish ladders.
The San Joaquin River, however, had a different fate.
Almost 60 mi (97 km) of the river is dry because of diversions from Friant Dam and Millerton Lake.
Even downstream of Mendota, where the Delta-Mendota Canal gives the river a new surge of water from the Sacramento-San Joaquin Delta, irrigation runoff water, contaminated with pesticides and fertilizer, has caused the river to become heavily polluted.
To make matters worse, efforts by the California Department of Fish and Game to route the San Joaquin salmon run into the Merced River in the 1950s failed, because the salmon did not recognize the Merced as their "home stream".

Not only on the San Joaquin River have CVP facilities wreaked environmental havoc.
On the Sacramento River, Red Bluff Diversion Dam in Tehama County, while not as large or as impacting as Friant Dam, was once a barrier to the migration of anadromous fish.
The original fish passage facilities of the dam continually experienced problems from the beginning of operation in 1966, and introduced species that prey on young smolt often gather at the base of the dam, which reduced the population of outmigrating juvenile salmon into the Pacific.
The Red Bluff Diversion Dam has since been replaced with a fish screen and pumping plant, thus allowing unimpaired passage through Red Bluff.
Further upstream, Keswick and Shasta Dams form total barriers to fish migration.
Even out of the Central Valley watershed, the CVP's diversion of water from the Trinity River from Lewiston Dam into Whiskeytown Lake has significantly hurt the Klamath River tributary's salmon run.
Over three-quarters of the river's flow is diverted through the Clear Creek Tunnel and away from the Trinity River, causing the river below the dam to become warm, silty, shallow and slow-flowing, attributes that hurt young salmon.
Furthermore, the Trinity Dam forms a blockade that prevents salmon from reaching about 109 miles (175 km) of upriver spawning grounds.
In the early years of the 21st century, the Bureau of Reclamation finally began to steadily increase the water flow downstream from Lewiston Dam.
While providing less water for the CVP altogether, the new flow regime allows operations to meet the line drawn by Reclamation itself in 1952 stating that at least 48% of the river's natural flow must be left untouched in order for Trinity River salmon to survive.
The lack of flow in the Trinity up to then was also a violation of the authorization that Congress made over the operation of the dam.
The "...legislation required that enough be left in the Trinity for in-basin needs, including preservation of the salmon fishery."

In the early years of the 21st century, the Bureau of Reclamation studied the feasibility of raising Shasta Dam.
One of the proposed heights was 18.5 feet (5.6 m) greater than its current size, thus increasing the storage capacity of Shasta Lake by 636,000 acre feet (784,000 dam³).
The agency also proposed a smaller raise of 6.5 ft (2.0 m) that would add 290,000 acre feet (360,000 dam³).
Previously, a 200 ft (61 m) raise of the dam, increasing storage to 13,890,000 acre feet (17,130,000 dam³), was considered, but deemed uneconomical.
When Shasta Dam was first built, it was actually planned to be two hundred feet higher than it is now, but Reclamation stopped construction at its present height because of a shortage of materials and workers during World War II.
The raising
Once, profuse runs of anadromous fish—salmon, steelhead, and others—migrated up the Sacramento and San Joaquin Rivers to spawn in great numbers. The construction of CVP dams on the two rivers and many of their major tributaries—namely Friant Dam and Shasta Dam—mostly ended the once-bountiful Central Valley salmon run. From north to south, the Sacramento upriver of Shasta Dam, the American upriver of Folsom Dam, the Stanislaus upriver of New Melones Dam, and the San Joaquin upriver of Mendota—have become inaccessible to migrating salmon. In three of these cases, it is because the dams are too high and their reservoirs too large for fish to bypass via fish ladders. The San Joaquin River, however, had a different fate. Almost 60 mi (97 km) of the river is dry because of diversions from Friant Dam and Millerton Lake. Even downstream of Mendota, where the Delta-Mendota Canal gives the river a new surge of water from the Sacramento-San Joaquin Delta, irrigation runoff water, contaminated with pesticides and fertilizer, has caused the river to become heavily polluted. To make matters worse, efforts by the California Department of Fish and Game to route the San Joaquin salmon run into the Merced River in the 1950s failed, because the salmon did not recognize the Merced as their "home stream".
Not only on the San Joaquin River have CVP facilities wreaked environmental havoc. On the Sacramento River, Red Bluff Diversion Dam in Tehama County, while not as large or as impacting as Friant Dam, was once a barrier to the migration of anadromous fish. The original fish passage facilities of the dam continually experienced problems from the beginning of operation in 1966, and introduced species that prey on young smolt often gather at the base of the dam, which reduced the population of outmigrating juvenile salmon into the Pacific. The Red Bluff Diversion Dam has since been replaced with a fish screen and pumping plant, thus allowing unimpaired passage through Red Bluff. Further upstream, Keswick and Shasta Dams form total barriers to fish migration. Even out of the Central Valley watershed, the CVP's diversion of water from the Trinity River from Lewiston Dam into Whiskeytown Lake has significantly hurt the Klamath River tributary's salmon run. Over three-quarters of the river's flow is diverted through the Clear Creek Tunnel and away from the Trinity River, causing the river below the dam to become warm, silty, shallow and slow-flowing, attributes that hurt young salmon. Furthermore, the Trinity Dam forms a blockade that prevents salmon from reaching about 109 miles (175 km) of upriver spawning grounds. In the early years of the 21st century, the Bureau of Reclamation finally began to steadily increase the water flow downstream from Lewiston Dam. While providing less water for the CVP altogether, the new flow regime allows operations to meet the line drawn by Reclamation itself in 1952 stating that at least 48% of the river's natural flow must be left untouched in order for Trinity River salmon to survive. The lack of flow in the Trinity up to then was also a violation of the authorization that Congress made over the operation of the dam. The "...legislation required that enough be left in the Trinity for in-basin needs, including preservation of the salmon fishery."
In the early years of the 21st century, the Bureau of Reclamation studied the feasibility of raising Shasta Dam. One of the proposed heights was 18.5 feet (5.6 m) greater than its current size, thus increasing the storage capacity of Shasta Lake by 636,000 acre feet (784,000 dam³). The agency also proposed a smaller raise of 6.5 ft (2.0 m) that would add 290,000 acre feet (360,000 dam³). Previously, a 200 ft (61 m) raise of the dam, increasing storage to 13,890,000 acre feet (17,130,000 dam³), was considered, but deemed uneconomical. When Shasta Dam was first built, it was actually planned to be two hundred feet higher than it is now, but Reclamation stopped construction at its present height because of a shortage of materials and workers during World War II. The raising 
Central Valley Project