Well its not a pretty story. Let me tell you a little bit about Humboldt and Trinity Counties in California. Jerry Rohde has written extensively on the subject in the North Coast Journal here. Tony Platt has written extensively on cultural conflict, genocide and grave robbing in Grave Matters: Excavating California's Buried Past. 2011 Heydey Books, Berkeley.

According to Rohde, the killing began soon after the white arrival in 1850. "Within weeks of their arrival on Humboldt Bay, whites had murdered their first Indians and destroyed their first Wiyot village (see “The Sonoma Gang” in the Sept. 11, 2008 Journal). For a while, at least near the coast, such killings were isolated incidents, but by the late 1850s their frequency and intensity had increased."

Indians were a problem because they inhabited or used areas in conflict with the white interests in mining, ranching and harvesting timber. Where there were conflicts there were killings. Militias were formed and the Army was activated. Entire villages were burned, their inhabitants slaughtered. The most well known incident was the Indian Island Massacre of 1860. In the middle of the night following a native dance, whites descended upon a village on Indian Island in Humboldt Bay. There, they hacked to death women, children, elderly, any and all residents of the site. The Indian Island Massacre was by no means an isolated event. Villages were destroyed based on reports that cattle were missing. These incidents gave rise to place names like Burnt Ranch, Bloody Creek, and Dead Indian Road (I borrowed This one from Klamath Falls, OR).

To make the tragedy of Indian Island even more bizarre, every square meter of the site was later looted by artifact collectors in Eureka. One collector dug and collected over 300 graves on Indian Island and one other site. That is, in part, the subject of Platt's book cited above.

By 1865, the first treaties were ratified and the reservations were established. The practices of systematic acculturation were instituted by the US government. Children were sent away to voc. tech. schools, attended local schools and churches, and began to lose their languages as technological change and cultural upheaval overwhelmed them. Remember all this is taking place while native populations were being ravaged by wave after wave of disease. By the 1880s natives were prohibited from speaking their languages, traditional dances became rarer, then stopped and traditional medicine and coming of age ceremonies waned. By 1900, traditional dances were rare, native architecture had been completely replaced by white building and the languages were going away fast.

It has only been recently that some of the abandoned traditional practices have been reactivated. Among the Hupa, Yurok, and Karuk the womens Flower Dance has been reawakened in areas where it was dormant for 80 years. Many other dances are now being conducted at sites that were inactive for over 100 years.

Edit: More words. Edit 2: even more words

While I cannot speak for California specifically, the West Coast tribes faced hardships at the hands of the government as well.

During the Puget Sound war, which included many native tribes involved in skirmishes in Northwestern Washington, the Nisqually and Suquamish and Duwamish peoples of central Puget Sound suffered particularly. The catalyst of the war was the Treaty of Medicine Creek of 1854. Negotiated by Washington Territory Governor Isaac Stevens, the treaty preserved Indian fishing rights, but took away prime Nisqually farm land and instead gave them very harsh, mountainous tarrain. Chief Leschi, chosen to negotiate the treaty with Stevens, was outraged and chose to fight rather than give up his land. While relatively few died during the "war", it all came to a cumulative end with the execution of Chief Leshci after the Battle of Seattle. Like in a lot of cases, treaties were broken and the Indians faced the consequences.

However, the tribes of the Northwest had it a bit easier in comparison to tribes farther east. The main concern for native tribes, rather than land, was fishing and game rights. While land was important since that is where they lived, they accepted reservations more...peacefully...as long as it kept their right for food in place.

Sources: http://www.amazon.com/Remembered-Drums-History-Puget-Indian/dp/093654614X

And the book I am currently reading: http://www.rakuten.com/prod/indians-of-the-pacific-northwest/230245117.html?listingId=243135664&s_kwcid=

From the people themselves: http://www.suquamish.nsn.us/HistoryCulture.aspx

And maybe a look at Wikipedia...