The Indigenous nations of the Sacramento-San Joaquin Delta region significantly affected European and American colonial history in California. The twisted waterways and wetlands of California’s Delta were a barrier to inland incursions by the Spanish soldiers and priests that had invaded and seized Indigenous homelands in the San Francisco Bay Area. Indeed, the Delta became an important place of refuge for Native people escaping the coastal missions, thus helping to perpetuate traditional culture and Indigenous populations.
Although Native peoples had resisted the Spanish takeover in the Bay Area from the beginning, the resistance stiffened when the Spanish and Mexicans sent punitive expeditions of soldiers into the Delta. Delta freedom fighters had noteworthy leaders and held their own even against the largest army ever assembled in Spanish or Mexican California.
Fierce resistance and refusal to go to the Bay Area missions—combined with plummeting “mission Indian” populations due to unhealthy conditions and epidemics—contributed to the Mexican government’s decision to discontinue the missions. And although some Delta nations aligned with landed European-American “barons,” the incessant Indian raiding of the coastal ranches caused the other ranch owners to not actively oppose the Americans during the Mexican American War.
Ancient, Populous, Interconnected Cultures Before the Spanish Invasion
Modern descendants of the early Native American inhabitants of California’s Delta region often say that they and their ancestors have been in the region “since time immemorial.” It’s an apropos phrase because it means “in the distant past; since beyond human memory or record.”
The diverse evidence gathered by cultural anthropologists and geographers, anthropological linguists, and archaeologists leads them to reach the same conclusion: Indigenous peoples have been connected to the Sacramento-San Joaquin Delta region since time immemorial. Scientific evidence suggests that Native peoples likely settled what is now the Delta region as many as 1,500 generations or 30,000 years ago and without question were living in the area when the Delta first formed some 300 generations or 7,000 years ago. They had settled into large, year-round towns within sovereign tribal territories at least 100 generations or 2,000 years ago—the same towns and nations that were in place when Spain invaded a mere dozen generations (less than 250 years) ago.
At the center of the Delta were wetlands inundated twice daily during high tides and flooded during the wet season, so the Delta core was not inhabited year-round by Native Americans. But the peripheries of the Delta were home to a very dense concentration of people—in general, it was the densest Indigenous population in the entire North American continent, exceeded only by the Aztec empire in Central Mexico. Populations were especially high on the east side of the Delta where rivers flowed in from the Sierra Nevada. Few, if any, non-agricultural economies in the world have achieved the success of the Delta Native nations.
Indigenous peoples in the Delta region lived cooperatively with the natural plants and animals that shared their territory. Their ceremonial cycles tracked closely with and helped maintain balance among productive landscapes and important plants and animals. They sustained local habitats and hundreds of key natural resources with carefully planned controlled burns, as well as strategic pruning, tilling and digging, weeding, sowing, transplanting, and selective harvesting.
Citizens of Native nations had different roles in their societies. Some people were spiritual or civil leaders and functionaries, others had special knowledge or skills or developed their talents to make certain tools. Each nation peacefully interacted with many other sovereign tribal nations via established trade, marriage, and ceremonial networks. Thus, the Indigenous nations of the Delta were sustained over many generations. (A fuller depiction of traditional Delta Indigenous lifeways before the arrival of Europeans can be found in my article “Deep History of the Delta).”
European Ships Sporadically Contacted California Coastal Natives
The colonization story began in the 1500s, 24 generations ago, when Spain invaded what we know as Mexico, stole Indigenous lands, and colonized the region. Brief European ship contacts with coastal California, such as that of Francis Drake on the Marin coast in 1579, included “discovery rituals” which laid the groundwork for the eventual taking of sovereign Indigenous homelands in California. Contrary to what most of us learned in elementary school, Native peoples knew about Europeans before they landed, initially welcomed them to their sovereign homelands and communities, and saw them as sources of valuable trade goods and power—that is, prior to repeated European demonstrations of violence and deceit (see Atkins and Bauer, We Are the Land, chapter 2).
The European seafarers inadvertently introduced “Old World” diseases to which Native Americans had little resistance and which long-established trade networks inevitably spread to Indigenous nations in the Delta. While the new diseases caused some depopulation and are recorded in Indigenous oral histories, for two centuries the European impacts upon California Indians, especially non-coastal “interior” tribal communities such as those in the Delta region, were relatively minor. Then all hell broke loose.
Spain Invaded and Occupied Coastal California as Far North as the San Francisco Bay Area
in the 1770s-90s, twelve generations ago, Spain invaded and colonized coastal California, primarily to protect Spanish colonial enterprises in Mexico from other European colonial nations expanding in North America. The Spanish Empire seized Indigenous lands and resources; separated the Natives from their homelands and traditional connections by bringing them into closed mission communities; used forced Native labor to create mission infrastructure and hoped they would soon create pueblos (towns); and strove to forcibly convert the Indians to Catholicism, Spanish language, and Spanish culture—a process now recognized as cultural genocide. The goal was to totally absorb Native people into Spanish colonial society to create self-supporting frontier communities as a buffer against other colonial powers—communities with assimilated and acculturated people of Indigenous descent filling the largest and lowest rung in the caste hierarchy.
Spain occupied the homelands of San Francisco Bay Area Indigenous nations west of the Delta, founded a presidio (garrison of soldiers) there, and established two mission communities. Mission San Francisco de Asís (also known as Mission Dolores) was established in 1776-7 on the desolate north end of the peninsula. Ten years later and forty miles southeast in the fertile Santa Clara (Silicon) Valley, Mission Santa Clara de Asís was founded.
The Spanish missionaries and soldiers quickly impacted Bay Area Native people by introducing diseases which had severe effects on Indigenous populations with no previous exposure or acquired resistance; by physically abusing and raping Native people; by introducing domestic livestock and forbidding traditional landscape management, thereby minimizing Indigenous foods, materials, and healing resources; and by disrupting intertribal ceremonial alliances, marriage/kin relationships, and trade networks. In the years immediately after the establishment of the initial two Bay Area missions, Indigenous men fought against the Spanish soldiers to protect sovereign Native homelands and lifeways. No willing Native converts/laborers went to the missions.
The Delta Became a Place of Refuge
Many Bay Area Natives “resisted with their feet” and fled to what Indigenous author Tsim Schneider calls “’places of refuge,’ where they could collect traditional foods, share stories, dance, and carry out old practices while simultaneously integrating new ones” (Atkins and Bauer, We Are the Land, page 81). Most of these places were in the hinterlands of the Marin Peninsula north of the Golden Gate or inland (east) in the Sacramento-San Joaquin Delta.
The labyrinth of waterways and extensive wetlands that comprised the Delta made it nearly impenetrable given the Spaniards’ lack of navigational/topographical knowledge, the limited mobility of horse-mounted or foot soldiers, and the drawbacks of the few small sailing vessels available to the Spaniards. Thus, the Delta was a barrier shielding refugees and dozens of interior Indigenous nations from the direct impacts of early Spanish colonialism in the Bay Area.
In the mid-1790s, many remaining Bay Area Indians agreed to baptism at the missions, apparently because “a critical mass of [Indigenous] people developed a sense that they had no alternative to joining the Spanish system in the face of ongoing high death rates from unknown diseases, selective arrests of resistance leaders, [loss of homeland resources and trade and tribal relationships,] and threats of damnation from some of the Franciscan priests.” (Milliken, Native Americans at Mission San Jose, page 33).
“The decision to reject mission life could be made a thousand times, but the decision to join a mission community could be made only once” (Milliken, A Time of Little Choice, page 11) because after baptism, “mission Indians” were prisoners under strict Spanish control. Baptized Natives were hunted down by Spanish soldiers if they attempted to return without permission to their hometowns or escaped inland to the California heartland. It is important to note, however, that because the early Bay Area mission economies were hard-pressed to feed their populations, it was routine to give baptized Indians seasonal passes to gather and hunt traditional foods in their homelands. These passes assisted the maintenance of traditional culture, especially if tribal homelands and towns were distant from the mission.
As Schneider points out in Archaeology of Refuge and Recourse, given the conditions and horrible death rates at the missions, it is not surprising that “anthropologists and historians attempting to document California’s remaining Indigenous cultures during the 1900s looked to the missions as one of the most destructive of California’s colonial regimes and the primary source of Native cultural loss and assimilation. The tale crafted by anthropologists was thus one of indoctrination and wholesale cultural destruction” (pages 5-6). Schneider, on the other hand, emphasizes how the Native peoples of the Bay Area “created outlets within and beyond colonial settlements to resist and endure colonialism” (page 6).
Spain Sought a New Supply of Indigenous Converts/Laborers from the Delta Region
It was difficult for the Spanish to recruit enough new converts to maintain the desired labor force at the missions given the number of runaways and especially the high death rates and low birth rates among the captive “mission Indians.” Therefore, the Spanish eventually looked to the Delta—both to bring back Bay Area Natives that had sought asylum there and as a fresh source of new converts/laborers from the Indigenous nations in the Delta heartland region.
In 1797-1801, twenty years after the founding of Mission San Francisco, Mission San José was established farther inland, in present-day Fremont. Its location was advantageous to recruiting Native converts/workers from the Delta and northern San Joaquin Valley because from that new mission, expeditions could skirt the flooded core and large waterways of the greater Delta and pass around its less-watered San Joaquin Delta, or south, side. Mission San José “would certainly have been built further inland, in the Livermore or Diablo valleys, were it not for Spanish concerns about the hostile Saclans only 25 miles further north” (Milliken, Native Americans at Mission San Jose, page 37).
The Saclan nation had gone to Mission San Francisco in 1795 yet fled soon after due to an epidemic at the crowded mission. The fugitive Saclan were joined by several hundred other Indian escapees and the Saclan led a fierce resistance from what is now west central Contra Costa county until 1801. The Saclan freedom fighters foreshadowed the coming years in which the Sacramento-San Joaquin Delta became the seat of resistance to Spanish—and later Mexican—colonialism. (Excerpted and adapted below are brief examples of important battles and occurrences, selected from my “Paradise Lost” article.
Indigenous Delta Nations and Refugees Resisted Colonial Intrusions
The Anizumne (Miwok-speakers from near modern Rio Vista) moved to Mission San José in 1812, but within a year many rejected captive mission life, escaped, and found refuge with the Unizumne (near Walnut Grove). Twelve Spanish soldiers and 100 “mission Indian” auxiliary forces were sent in boats to retrieve the escapees. They engaged the Native defenders from four local nations in one of the first battles in the Sacramento River Delta. The number of Native men killed or wounded was not reported, but the soldiers and auxiliaries returned to Mission San José with no fugitive Anizumne in custody.
In the 1810s and ‘20s, Miwok-speaking nations from the lower Mokelumne River (for example, the Muquelemne from near Lodi), the lower Cosumnes River (such as the Cosomne from south of Elk Grove), and the Sacramento River Delta (including the Ochejamne and Unizumne from near modern Courtland and Walnut Grove) strongly resisted Spanish intrusions and protected Bay Area Native refugees. These powerful nations—and some Yokuts-speaking nations farther south along the Stanislaus River and the San Joaquin Delta—were sometimes called the “horse thief Indians” because of their mounted raids upon the mission herds.
Forty additional soldiers were assigned to the San Francisco presidio to thwart the raids by Delta heartland Natives. Many of the Spanish punitive expeditions that followed were not documented, but one attack in late 1819, for example, killed 27 Muquelemne, wounded 20 others, and took 16 captives.
A village near present-day Stockton was attacked by 25 soldiers backed up by “mission Indian” auxiliaries in 1818. Twenty-seven villagers were murdered. “Those who did not fall into our hands escaped into the brush,” wrote one Spanish soldier. “There must have been many wounded among them. After firing a rifle volley at them we charged with our lances and slaughtered them.” About 50 Natives were taken to the presidio at San Francisco, where they “were put at hard labor—at that time the main quarters were being built” (Cook, “Colonial Expeditions to the Interior,” page 196).
In 1826, the Cosomne nation (south of modern Elk Grove) routed a large invading force of soldiers from the San Francisco presidio. Later that year, the Mexicans returned with more soldiers and cannons, killed 41 Cosomne men, women, and children and took 40 women and children as slaves.
Estanislao’s Freedom Fighters Repelled the Largest Army in Hispanic California
The so-called “Estanislao’s Rebellion,” the topic of my prior article “Homeland Defense,” began in 1828 when hundreds of Indians escaped from Missions San José, Santa Clara de Asís, and San Juan Bautista and returned to their homelands on the Stanislaus River and the San Joaquin Delta. They formed a loose multi-national band of freedom fighters dedicated to keeping the Mexicans on the coast and out of the Delta and northern San Joaquin Valley. The Native patriots were led by a Lacquisemne man named Cucunuchi—renamed Estanislao at Mission San José in 1821—and a Josemite man named Huhuyut and renamed Cipriano at Mission Santa Clara. (The Lacquisemne were a Yokuts-speaking nation from near present Ripon; the Josemite were from near Vernalis.)
In November 1828, the insurgents soundly defeated Mexican soldiers sent to chastise them and force their return. In early May 1829, after the wet season, during which travel was impossible, the Native patriots were again victorious in a larger battle, primarily because they had built defensive earthworks and gathered a large fighting force. In late May, the largest army ever assembled in Hispanic California—104 soldiers from the presidios at Monterey and San Francisco, 50 “mission Indian” auxiliaries, plus citizen volunteers—was deployed by the Father-President of the missions and the commander of the San Francisco presidio. The imposing Mexican army used cannons and set the dense woods on fire, but the third and final battle was a draw, the Native freedom fighters neither conceded their territory nor surrendered.
The recruitment of new converts/laborers at the Bay Area missions drastically declined and did not increase for five or more years after the Estanislao battles. This decline influenced Mexico’s decision to discontinue the mission system.
The Stanislaus River and Stanislaus County were later named for the Indigenous leader Cucunuchi/Estanislao.
Estanislao belongs with King Philip [Metacomet, from Massachusetts], Tecumseh, Pontiac, and Geronimo, as an outstanding Indian chief who fought the white man with persistence and daring. Like many another champion…he was, depending on your point of view, a patriot to be venerated or a bandit to be [denounced]. To the…historian he is of interest as by far the most able military and political leader produced by the [Indigenous peoples] in California (Cook, “Colonial Expeditions to the Interior,” page 165.)
Delta Resistance Was Weakened by Attrition, Changing Alliances, Catastrophic Epidemic
Two years later, in 1830, a boat expedition from Mission San José went up the Sacramento River seeking mission escapees. When the Ochejamne (near Courtland) refused to give up fugitives they had taken in, the Mexican soldiers recruited odd allies to bolster their forces: members of nearby Miwok-speaking nations including the Cosomne, Ylamne, and Siusumne. Because those nations had traditionally been trading partners or associates of the Ochejamne, the alliance with the Mexicans indicated a rift among former allies and illustrates the volatility of the historic period, characterized by constantly shifting conditions upon which Indigenous nations had to base decisions.
The allied Mexican-Native nations attacked, but the Ochejamne forced them to retreat with several wounded men. As luck would have it, the Mexicans encountered and enlisted another group of allies: eleven American trappers. The Mexicans, Americans, and allied Natives attacked and forced the Ochejamne to burn their own village and retreat into the Delta. Within months, more than 300 members of the Ochejamne nation moved to Mission San José, the largest single group from the Delta or Central Valley to be baptized at any Bay Area mission.
In 1832-33, nine and a half generations ago, Hudson’s Bay trappers unwittingly brought malaria from Oregon country into the mosquito-filled wetlands of California’s Central Valley. Within months, 75-80 per cent of Delta and Valley Indians died from the epidemic, one of the most catastrophic plagues in California history. The depopulation caused significant shifting of Native territories and alliances and caused many Delta peoples to move to missions.
Indigenous Peoples Were Minimally Paid Laborers for Townsfolk and Landed “Barons”
A group of Mexican citizens from the pueblo (civilian town) near Mission Santa Clara (modern City of San Jose) in 1833 sought to return Indian runaways—the pueblo’s minimally paid laborers—and to punish Natives from the interior for raiding the herds of the missions and pueblos. The vigilantes arranged a meeting with the powerful Muquelemne nation that had provided sanctuary to refugees and was the predominant raiding nation. During the meeting, the Mexicans suddenly attacked—even though most of the Muquelemne were not armed—and at least 22 Natives were killed. The Calaveras River may have been named for the Indigenous bodies left at the site of this treachery and massacre, perhaps left unburied because of the malaria epidemic (calaveras is “skull” in Spanish).
In 1837-38, a smallpox epidemic that originated at Fort Ross, the Russian settlement on the Sonoma coast, spread through the Bay Area, encouraging the rapid dispersal of remaining “mission Indians” as Mexico discontinued or secularized the missions. Some “mission Indians” with homelands in the Delta formed new multi-national Indigenous communities—for example, one on the Sacramento River was comprised of Gualacomne, Ochejamne, and Chupumne refugees, another west of Pleasanton was even more diverse. Some Native people returned to the vicinity of their original homelands in the Delta, but none reestablished control of tribal territories. Indigenous homelands in and adjacent to the Delta became “public domain”—some given away as land grants by the Mexican government, some later sold by the State of California.
American John Marsh acquired a land grant on the east base of Mt. Diablo near modern Brentwood, in the homelands of the Bay Miwok-speaking Volvon nation. When Mission San José was discontinued in 1837-39, the captive Indians were turned out and many—including many originally from the Delta—moved to Marsh’s ranch.
Marsh was a booster encouraging American settlers to come to California. He wrote to Missourians:
In many instances when a family of white people have taken a farm in the vicinity…in a short time they would have a whole tribe as willing serfs. They submit to flagellation with more humility than the negroes. Nothing more is necessary for their complete subjugation, but kindness in the beginning, and a little well timed severity when manifestly deserved…. Throughout all California the Indians are the principal laborers, without them the business of the country could hardly be carried on (Milliken, Native Americans at Mission San Jose, page 76).
In recognition of Mariano Vallejo’s service in the final battle with the Indigenous insurgents in “Estanislao’s Rebellion,” he was granted 66,600-acre Rancho de Petaluma (in ten years the ranch would grow to 175,000 acres). The colonial influence exerted over Delta Natives by the Bay Area missions waned and was assumed by Vallejo. His influence extended to the lower Sacramento River and the Sacramento River Delta.
Vallejo entered a “mutual defense pact” with the Delta Ochejamne and Siusumne nations in 1837. A year later, those nations attacked the Muqulemne and retrieved horses stolen from Vallejo. Muqulemne raiders were soon also defeated at the entrance to the Napa Valley before they had reached Sonoma pueblo.
The following year, 1839, Swiss expatriate John Sutter and a small group including eight or ten Native Hawaiians traveled by boats through the Delta to establish New Helvetia, a “feudal barony,” an agricultural/trading enterprise headquartered near the confluence of the American and Sacramento Rivers (now Sacramento). It was near the Indigenous Nisenan towns Pusune and Sicomne. The land grant “barony” soon expanded north up the Sacramento Valley to include the significant Nisenan town Hok, on the Feather River near its confluence with the Bear River, south of modern Yuba City.
The Nisenan had been less impacted by the Bay Area missions than other Delta Indigenous nations because the Delta wetlands and the freedom-fighting nations on the south and east edges of the Delta were a barrier to Spanish/Mexican intrusions. Many Nisenan, along with Miwok- and Yokuts-speaking people from the Delta, eventually became minimally-paid workers or serfs—some researchers consider them slaves—for Sutter: his trappers, soldiers, herdsmen, farm laborers, craftsmen, etc.
The Cosomne, from their homelands along the Cosumnes River south of modern Elk Grove, twice attacked New Helvetia shortly after its founding, trying to displace Sutter. Both attempts failed because Sutter had brought three cannons, and muskets, rifles, powder, and shot with which to defend his empire. Thus, colonial power shifted from Vallejo and several Sacramento River Delta Indigenous nations realigned with Sutter.
In 1840, the Ochejamne participated in a raid in the Napa Valley and they abandoned their homeland in the Sacramento River Delta to live near New Helvetia. That same year, Sutter recruited the remaining members of the Gualacomne (a large nation south of present Freeport) to join with the Ochejamne and attacked and defeated the Cosomne. After that defeat, many members of the large Cosomne nation moved to Mission San José and by 1844, those that remained had moved to live near Sutter’s Fort.
The Muquelemne took control of former Cosomne homelands along the Cosumnes River. In 1843, they established a village on the Cosumnes River at which they farmed until at least 1855. The Muquelemne provided about 100 warriors to serve under Sutter in support of Mexican governor Micheltorena in 1845. Nevertheless, in 1846, Sutter attacked and killed many Muquelemne near the Calaveras River, east of modern Stockton.
Delta Indigenous Warriors and Raiders Assisted the U.S. Takeover of California
The United States declared war on Mexico in 1846 and coincidently (or not) John Frèmont and his heavily armed U.S. Expedition arrived at Sutter’s New Helvetia. Sutter and his Native allies supported the Americans against Mexico. More than 30 Indigenous men joined the California Battalion commanded by Frèmont, including men from Delta Indigenous nations such as the Muquelemne, Cosomne, Ochejamne, Gualacomne, and Ylamne.
Natives from the Delta and northern San Joaquin Valley also helped the takeover by the United States in another way. Decades of Indian resistance and raiding had left many Coastal Range ranches
in a condition of economic ruin. The loss of large numbers of horses and mules deprived the [ranch owners] of the means to work their herds of cattle. For some Californios [Californians of Spanish descent], protecting their ranchos from Indian raiders took precedent over defending their territory against American invaders. Others concluded that only with a change of government would Indian raiding be brought to an end. Realizing the hopelessness of their situation, many Californios thus accepted, if not welcomed, the American takeover (Phillips, Indians and Intruders, pages 164-65).
The Gold Rush Resulted in Murder and Genocide but Indigenous Cultures Survived
The Euro-American discovery of gold in Nisenan territory in 1848, eight and a half generations ago, and the resulting international Gold Rush continued negative impacts upon the remaining Delta Indigenous people. Delta rivers provided the primary transportation between San Francisco, Sacramento City (gateway to the Northern Mines), and Stockton (gateway to the Southern Mines)—then the three largest cities in California. Stockton founder Charles Weber and partners formed the first California mining company in 1848 and employed more than 1,000 Indigenous people to pan for gold in the placers; most of those Native laborers were originally from the east and southeast periphery of the Delta. Later, with the arrival of Oregonians, who were extremely bigoted towards Native Americans, Indians were expelled from the gold camps, murdered by individual argonauts, and eventually killed by State- and Federal-sponsored genocide campaigns and bounties.
It is a testament to the strength, resiliency, and perseverance of Delta Indigenous peoples that they and their rich cultures survived to the present day. It is noteworthy that several Tribes are contributing to the planning, development, management, and storytelling of the new Sacramento-San Joaquin Delta National Heritage Area.
David Stuart recently retired as the executive director of the San Joaquin County Historical Society. Previously, he directed the Sacramento History Museum, the Sacramento Science Center, and museums in Ventura. His family settled in the Delta in 1860.