For a river of its size, the Sacramento is considered to have fairly clean water.
However, pollutants still flow into the river from many of its tributaries and man-made drains or channels.
Pesticide runoff, especially DDT, is one of the largest problems faced today, because of the valley's primarily agricultural economy.
Increased erosion caused by the removal of riparian vegetation and the runoff of fertilizers into the river have led to occasional algae blooms, though the water is usually cold because of the regulation of dams upstream.
Other pollutant sources include urban runoff, mercury and even rocket fuel that was reported to have leaked near the American River from an Aerojet extraction project.

Mercury pollution created by mining and processing activities during the California Gold Rush still has a profound impact on the Sacramento River's environment.
The toxic substance was widely used by miners to separate gold from the surrounding rocks and dirt, and was disposed of by allowing it to evaporate.
Most of the mercury was mined in the Coast Ranges to the west of the Sacramento River; mines in these mountains produced roughly 140,000 tons of mercury to serve the Gold Rush.
When the gold rush ended, most of the mines were closed but toxic acidic water and chemicals continue to leak from within, into west-side Sacramento tributaries such as Cache Creek and Putah Creek.
In the east, mercury that permeated into the ground has contaminated several aquifers that feed rivers such as the Feather, Yuba and American.
Even the evaporated mercury posed problems – so much of it was used that significant concentrations still linger in the air in many places.
Mercury pollution continues today and will probably continue for decades or centuries into the future.

In July 1991, a train derailed near Dunsmuir, California alongside the Sacramento River.
A tank car split open, spilling about 19,500 gallons of the pesticide metam sodium into the river.
The chemical formed a stinking, bubbling, green glob that moved 45 miles (72 km) down the river, killing everything in its path.
More than one million fish were killed, including at least 100,000 rainbow trout, and thousands of other aquatic creatures as well as nearby trees.
Next, the green glob entered Shasta Lake, California's largest reservoir.
Fortunately, a system of aerating pipes at the bottom of the lake had been set up to dissipate the chemical, reducing it to almost nothing by the 29th, preventing further environmental destruction.
The tank car carrying the metam sodium through California was of a type that the National Transportation Safety Board said had "a high incidence of failure" in accidents.
Furthermore, the tank car was not labeled, so the train's crew was unaware of the danger posed by the chemical.
For a river of its size, the Sacramento is considered to have fairly clean water. However, pollutants still flow into the river from many of its tributaries and man-made drains or channels. Pesticide runoff, especially DDT, is one of the largest problems faced today, because of the valley's primarily agricultural economy. Increased erosion caused by the removal of riparian vegetation and the runoff of fertilizers into the river have led to occasional algae blooms, though the water is usually cold because of the regulation of dams upstream. Other pollutant sources include urban runoff, mercury and even rocket fuel that was reported to have leaked near the American River from an Aerojet extraction project.
Mercury pollution created by mining and processing activities during the California Gold Rush still has a profound impact on the Sacramento River's environment. The toxic substance was widely used by miners to separate gold from the surrounding rocks and dirt, and was disposed of by allowing it to evaporate. Most of the mercury was mined in the Coast Ranges to the west of the Sacramento River; mines in these mountains produced roughly 140,000 tons of mercury to serve the Gold Rush. When the gold rush ended, most of the mines were closed but toxic acidic water and chemicals continue to leak from within, into west-side Sacramento tributaries such as Cache Creek and Putah Creek. In the east, mercury that permeated into the ground has contaminated several aquifers that feed rivers such as the Feather, Yuba and American. Even the evaporated mercury posed problems – so much of it was used that significant concentrations still linger in the air in many places. Mercury pollution continues today and will probably continue for decades or centuries into the future.
In July 1991, a train derailed near Dunsmuir, California alongside the Sacramento River. A tank car split open, spilling about 19,500 gallons of the pesticide metam sodium into the river. The chemical formed a stinking, bubbling, green glob that moved 45 miles (72 km) down the river, killing everything in its path. More than one million fish were killed, including at least 100,000 rainbow trout, and thousands of other aquatic creatures as well as nearby trees. Next, the green glob entered Shasta Lake, California's largest reservoir. Fortunately, a system of aerating pipes at the bottom of the lake had been set up to dissipate the chemical, reducing it to almost nothing by the 29th, preventing further environmental destruction. The tank car carrying the metam sodium through California was of a type that the National Transportation Safety Board said had "a high incidence of failure" in accidents. Furthermore, the tank car was not labeled, so the train's crew was unaware of the danger posed by the chemical.
Sacramento River