Lead.
The Calaveras River is a river in the San Joaquin Valley of California.
It flows roughly southwest for from the confluence of its north and south forks in Calaveras County to its confluence with the San Joaquin River in the city of Stockton.
In the past, it has been used for agriculture and irrigation, drinking water, and for recreational purposes. There have been many improvement projects on the Calaveras River to address its pollution and efficiency for local residents.
Background information.
The Spanish word "calaveras" means "skulls." The river was said to have been named by Spanish explorer Gabriel Moraga in 1806 when he found many skulls of Native Americans along its banks. He believed they had either died of famine or been killed in tribal conflicts over hunting and fishing grounds.
Later, human remains were of the native Miwuk people killed by Spanish soldiers after they banded together to rise against Spanish missionaries. The Stanislaus River is named for Estanislau, a coastal Miwuk who escaped from Mission San Jose in the late 1830s. He is reported to have raised a small group of men with crude weapons, hiding in the foothills when the Spanish attacked. The Miwuk were quickly decimated by Spanish gunfire.
In 1836, John Marsh, Jose Noriega, and a party of men, went exploring in Northern California. They made camp along a river bed in the evening, and when they woke up the next morning, discovered that they had camped in the midst of a great quantity of skulls and bones. They also gave the river the appropriate name: Calaveras.
Surrounding geography.
New Hogan Lake is the only lake on the river. It is formed by New Hogan Dam, which was completed in 1963. The dam was built by the United States Army Corps of Engineers, primarily for flood control. The dam also provides drinking water, water for irrigation, hydroelectricity and recreation, including fishing, camping, swimming and water skiing. 
Downstream from the Calaveras River is Mildred Island, a submerged island that also provides recreation such as fishing. 
The Mormon Slough, a distributary of the Calaveras, splits away about five miles east of Linden, California. In east Stockton, the Stockton Diverting Canal reconnects the Mormon Slough and the Calaveras. Downstream from this flood control channel, the often dry Mormon Slough continues on its southerly path, through downtown, to the Stockton Channel. The Calaveras makes a northerly arc, passing through farmland, orchards, and the University of the Pacific Stockton Campus, then alongside its namesake Brookside district, before flowing into the Deepwater Channel about three miles downriver from the Mormon Slough. Thus much of central Stockton, being completely surrounded by these waterways, is itself one of the many river islands which make up the San Joaquin Delta.
The Delta.
The Sacramento River meets the San Joaquin River in what is known as "The Delta" between Lodi, California, and the Carquinez Strait. Deltas are a geographical feature where river water flows and branches out into a larger, flatter area. However, the Sacramento-San Joaquin Delta is special because instead of splitting into multiple channels as water flows downstream, multiple channels are coming together.
Hundreds of thousands of people are licensed to fish in the Bay Area and Delta regions, and 90% of people from low-income communities depend on fish from these rivers for food. The Calaveras River has various species of fish that people catch, eat, and even some that are federally protected such as steelhead and rainbow trout.
Past Contaminants.
Chemicals.
Since the California Gold Rush of the Mid-1800s, water running through the state has been introduced to mercury and other industrial chemicals. Per-and Polyfluoroakyl substances (PFAs)  are man-made chemicals designed to make products stain and water resistant, but are of concern to the environment because of their difficulty to be decomposed. They are a class of chemicals known as forever chemicals that don’t get degraded well naturally and tend to stay in the environment including in the soil, air, and water.
As the Calaveras River is used for agriculture, use of pesticides and herbicides also impact cleanliness of the water. Although present in small amounts, diazinon and chlorpyrifos are toxic to water life. Organophosphate pesticides are brought to the water by seasonal stormwater runoff. Poor drainage for soils and the amount of pesticides farmers are using affect the water to varying degrees. Since learning about the effect of pesticides, farmers have started to reduce the use of them either by switching to more organic options, diluting the chemicals, etc.
There have been hazardous material spills in the past from maintenance issues such as sewers overflowing as well as recreational accidents such as fuel spills from boats and vehicles.
Neon Algae Blooms.
Cyanobacteria (blue green algae) can grow anywhere in the world, but they are especially harmful when they produce toxins. Producing toxins, blocking sunlight by dense blooms and potentially using up all the oxygen in the water are many ways in which aquatic life is harmed. For the Calaveras River, the first algal bloom was found April 2019 in the New Hogan Reservoir but it was resolved by June 2019.
Past improvement plans.
Many improvement projects have been done in the past to better the Calaveras River for residents and its inhabitants.
In 2014, the Calaveras River was struggling to house natural wildlife because of its past diversions that spread the river water too thin. The U.S. Fish and Wildlife Service worked with residents to restore bridges and rebuild structures that would serve to connect residents on both sides of the river while not inhibiting the natural migration of fish species, the Caprini Crossing for example. After these restorations, the river was able to produce more salmon and steelhead, considerable amounts for the relatively small system that is the Calaveras River.
2020 Calaveras River Conservation Plan.
In 2020, the Stockton East Water District planned out a program that would protect the threatened Central Valley steelhead, endangered Chinook salmon, and more natural wildlife. They called this the 2020 Calaveras River Conservation Plan. It was the first habitat conservation plan in the Central Valley to be approved by the National Marine Fisheries Service. The program helped federally protected species and helped to maintain water quality of the Calaveras River.
References.
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