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The Calaveras River is a 51.9 mi long river in Northern California in the United States. It drains part of the western Sierra Nevada foothills, flowing west across the agricultural San Joaquin Valley into the San Joaquin River at Stockton. The Calaveras River watershed drains 470 mi2 and is primarily in Calaveras and San Joaquin Counties, although a small portion is in Stanislaus County. The river is a major source for irrigation water supply and groundwater recharge, and is dammed to form New Hogan Lake. The Spanish word calaveras means "skulls" and was given to the river in the early 1800s by explorers who found remains of numerous Native Americans along its banks.

Geography
The Calaveras begins as a number of creeks draining the Sierra Nevada along the western edge of the Stanislaus National Forest, in Calaveras County. The North and South Forks of the river are formed in the foothills near the town of San Andreas by the confluence of several creeks. The North Fork, beginning at 3800 ft above sea level, is fed by Esperanza, Jesus Maria and Murray Creeks in the Mokelumne Hill area. The South Fork is formed by the confluence of San Domingo and Cherokee Creeks; San Domingo, the larger tributary, originates near Hathaway Pines at about 3400 ft. Other tributaries of the South Fork include San Antonio, Calaveritas and Willow Creeks. San Antonio Creek begins at the highest point of the Calaveras watershed, about 5800 ft at Camp Connell. A tributary of San Antonio Creek, Big Trees Creek, flows through Calaveras Big Trees State Park.

In the foothills, the North Fork and South Fork form the Calaveras River which flows into New Hogan Lake, formed by the New Hogan Dam. Below the dam the Calaveras River flows west past Rancho Calaveras and Jenny Lind. It crosses very briefly into Stanislaus County before entering San Joaquin County, where it flows through farmland in the Central Valley. East of Linden, it splits to form a distributary, Mormon Slough, which flows into the San Joaquin River at the Port of Stockton. The main stem continues west past Waterloo, flowing through the northern suburbs of Stockton, where it bisects the University of the Pacific campus and is crossed by Highway 99 and Interstate 5. It joins the San Joaquin River in the Sacramento–San Joaquin River Delta, west of Country Club, about 37 mi from where the San Joaquin ends at Suisun Bay. The lower part of the Calaveras River forms a narrow tidal estuary; however, the once extensive wetlands in the area were mostly drained for agriculture in the 19th and early 20th century.

The Calaveras River is small compared to other Sierra rivers flowing into the Central Valley, such as the Mokelumne and Stanislaus Rivers, whose watersheds adjoin that of the Calaveras on the north and the south, respectively. The river drains a relatively modest 470 mi2, at elevations mostly below 5000 ft. About 363 mi2, or more than three-quarters of the watershed, is above New Hogan Dam. It is the second smallest Sierra Nevada watershed, larger only than the Bear River. The primary contributor to river flow is rainfall, not snowmelt. The average annual runoff is 166000 acre feet, with 90000 acre feet, slightly over half of the total, flowing into Mormon Slough and the rest into the Lower Calaveras River.

The average discharge below New Hogan Dam between 1907 and 1990 is 227 cuft/s, with a maximum of 649 cuft/s in February and a minimum of 19 cuft/s in October. The all-time highest flow was 50000 cuft/s on January 31, 1911, ; on the other hand before damming, the river frequently dried up in the late summer and fall of dry years. The highest flow since the construction of New Hogan Dam was 10000 cuft/s on January 22, 1980.

Geology
The bedrock below the Calaveras River watershed consists of highly fractured and folded igneous and metamorphic rock. The Rescue Lineament-Bear Mountains fault zone bisects the watershed and anchors the gold-bearing formations of the Mother Lode.

The evolution of the area began about 400 million years ago, when the Sierra Nevada mountains were first formed by forces along the North American and Pacific Plates. The fissures created by the folding rock were filled with molten granite and gold-bearing quartz. As the ancient Calaveras River eroded into the rock the quartz veins were exposed and the gold carried into the downstream river bed. These gold deposits were later buried as the river changed course.

Native Americans
Prior to European contact, the main Native American groups living along the Calaveras River were the Miwok and Yokuts, who are believed to be descended from Great Basin peoples about 2,000–3,000 years ago. The people of the Calaveras River valley spoke the Northern Sierra Miwok language. The native names for the river was the Yachekumna, and marked the northern boundary of the territory of the Yacheko tribe of Miwok. The Yachekos' main village was located near present-day Stockton, at the confluence of the San Joaquin and Calaveras Rivers.

Around 1832, fur trapper Juan Jose Warner described the Calaveras River Miwok as the most "hostile-disposed" of the area.

Known Native American villages along the Calaveras River include Apautawilü north of the river; Heina, Newichu, Kechenü, Kaitimü, and Mona-sü in the headwaters, and Humata and Katuka along tributaries of the river.

Archaeological studies have revealed evidence of human habitation as long as 12,000 years ago, but little is known about these early peoples.

Exploration and naming
The Calaveras River was named by Spanish explorer Gabriel Moraga in 1806 who saw many skulls of Native Americans along its banks. Moraga and his expedition were the first Europeans to make contact with the local peoples. However, another account credits John Marsh and Jose Noriega with the naming of the Calaveras River much later, around 1836. Their party had camped along the river and awoke to find "numerous bones and skulls of men."

There are at least two explanations for the origin of the bones. They may have been an ancient burial ground, for those killed in a battle between the Yachekos and Siyakumnas tribes. Native peoples of the area usually buried their dead in earthen mounds, so the bones may have been exposed by erosion from rain or flooding of the Calaveras River. This is the most likely explanation for the bones found by Moraga in 1806. The second account suggests that the skeletons were the casualties of fighting between the Spanish army and Native Americans led by Estanislao, a Yokuts chief, who escaped from the Mission San José in 1827 with about 400 other Native Americans that had been pressed into colonial service.

When the Spanish settled California they established numerous missions or religious outposts; although none were in the Central Valley where the Calaveras River is located, many Native Americans in the Calaveras River area were conscripted to perform labor in Spanish settlements and to be converted to Christianity, with varying degrees of success. The missions were secularized following the independence of Mexico from Spain in 1821, but the harsh working conditions continued and many native peoples desired to rebel and return to their old way of life.

In the years after Estanislao's escape, his men terrorized the San José, Santa Clara and Santa Cruz missions, as well as other Mexican settlements throughout Central California. Joining with other Yokuts, Miwok and Chumash, Estanislao's forces grew to over 4,000 before the Mexican government responded, sending an army led by General Mariano Guadalupe Vallejo into the area in 1829. The Native Americans were ultimately defeated by Spanish gunfire on the nearby Stanislaus River in 1828.

Gold Rush
During the California Gold Rush in the 1850s, the Calaveras River was one of the richest gold bearing streams of the Mother Lode. Hydraulic mining was carried out in several places in the upper Calaveras River watershed. Hundreds of thousands of cubic yards (cubic metres) of mine tailings still remain along the Calaveras River, especially in the area just below New Hogan Dam. The booming gold industry was a major factor in the creation of Calaveras County in 1850. Most of the communities in the area today retain their names from the Gold Rush period.

San Andreas, today the largest town in the upper Calaveras River watershed, was originally settled by Mexican miners in 1848. Although local placer or river-bed gold was mined out within a few years, the discovery of gold bearing sediments in ancient, abandoned channels of the Calaveras River kept the mining economy going for many more years. Gold mined in the area funded efforts of the Union Army during the Civil War in the 1860s. San Andreas became the Calaveras County seat in 1866. San Andreas was also known as a "breeding ground for bandits". For a while the area was terrorized by the notorious Joaquin Murrieta and his gang; in 1853 Murrieta was captured and killed by California Rangers who then collected a $6,000 bounty ($174,000 in 2013 dollars) for his head. Highwayman Black Bart, who robbed stagecoaches in Calaveras County for eight years, was tried and sent to prison here in 1883.

The mining town of Petersburg, also known as Greasertown, was also a major economic center during the Gold Rush and during its brief history was known for its racial conflicts. During the late 1850s, the town was made up mostly of Chinese miners, who took over the "played-out" claims left by other miners who had previously given up and left. In May 1859 Chinese and white miners fought for control of a dam, resulting in some serious injuries. On September 14, 1852 the town was destroyed by a fire, which was blamed on Mexican or Chilean immigrants. A number of miners from the surrounding area banded together to drive away the Spanish-speaking population. The town suffered another severe fire in July 1854.

After severe flooding in 1907, the city of Stockton proposed to dam the Calaveras River above Jenny Lind. Petersburg, which lay in what would become the new reservoir was demolished on June 25, 1924. The dam and reservoir were named for city engineer Walter Byron Hogan. In 1964 the larger New Hogan Dam was completed to replace the old dam.

Flora and fauna
The channel of the lower river is often choked with invasive plants such as Arundo donax (giant reed) and water hyacinth.

River modifications
The original Hogan Dam, a concrete thin-arch dam, was built in 1930 to provide flood control. The old dam was 136 ft high, 1325 ft long and held 115000 acre feet of water when full. The New Hogan Dam, a larger earth-fill structure was authorized by Congress in 1944 for the additional purposes of irrigation and municipal water supply. However, the new dam was not completed until 1964. The New Hogan Dam, 210 ft high and 1960 ft long, has a capacity of 317100 acre feet of water.

The original dam still exists, underwater about 500 ft upstream from the present dam. It occasionally reappears during severe droughts, most recently in 2015.

Much of the lower Calaveras River has been straightened, widened and channelized to increase its hydraulic capacity. The US Army Corps of Engineers considers the Calaveras River navigable from the mouth to 2000 ft upstream of Interstate 5, a distance of approximately 2 mi.