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The Yuba River Basin has not always looked the way it does today. In fact, the coastline of the North American continent once lay east of the Sierra Nevada, and the rest of California was nothing but open sea. Not until about 200 million years ago did the bedrock of this area, which geologists call a terrane, come sailing in and dock onto the continent. This particular terrane is a mess of ocean-floor sediments—clay, sand, limestone. As the subducting ocean crust slid underneath the continental plate, the sediments were crushed and cooked in the trench between the two plates, transformed into slate, schist, quartzite, and marble, and then accreted onto the continent's edge.

As the ocean crust sank, it heated up and melted the rocks above it. The melted continental crust rose up toward the surface and, as it cooled, formed an enormous underground expanse of granite called the Sierra Nevada Batholith. The batholith, with a surface area of 25 thousand square miles, was exposed over subsequent millions of years as the rocks on top gradually eroded away.

Up until just a few million years ago, the Sierra Nevada Mountains were nothing but a broad, rolling lowland. The lowland was drained by an ancient river system carrying enormous amounts of sediment westward toward an inland sea where the Sacramento valley now lies. This sediment, including gold-bearing gravels, was deposited in a broad flood plain in the area of the present Yuba River. During the Miocene and Pliocene eras, between 25 and 2 million years ago, the land to the east began to stretch apart and break into blocks, and the Sierra was the western-most block to uplift. The block tilted westward as it rose, creating a steep eastern face and a more gradually inclined western slope; in fact, it is still rising today. Around that same time, between 25 and 2 million years ago, intermittent volcanism spread volcanic ash and mudflows over much of the landscape.

As the mountains rose, the river that would one day be named the Yuba began to flow more and more swiftly, cutting the deep canyon we see today. Ice ages during the Pleistocene brought the advance and retreat of countless glaciers which scraped away much of the volcanic rock and left the smooth, polished granite boulders that characterize the present riverbed.