Three million years ago, the Colorado River, which emptied into the Gulf of California, deposited enough layers of sediment to separate the Salton Sink from the Gulf of California creating a large ancient lake called Lake Cahuilla. To the west, the southern portion of the San Diego coast was still underwater. Movements from the Rose Canyon Fault stretched out the bulge of land in the La Jolla area just above Crown Point. Just to the west of Point Loma, below the waters, a system of cross faults called the Silver Strand, Coronado, and Spanish Bight Faults pushed up two low clumps of land: North Island, and Coronado. Four smaller islands to the southwest were also pushed up by other cross faults in the process: Mexico’s Los Coronados Islands. These lands wouldn't be exposed until sea levels once again fell however.

By about two million years ago, the mountain ranges were starting to erode into their present look. Lake Cahuilla began a cycle of evaporating and refilling, as it dried, it would leave huge layers of salt deposits on the desert sand. Back to the west, ocean levels finally fell, exposing the smooth land underneath, and shrinking the enormous bay to more of its present size. Other rivers created around this time include the San Luis River, the Sweetwater River, the Otay River, and the Tijuana River. Other various valleys suggest that there may have been more rivers at one time, including down Telegraph Canyon and Chollas Creek. Thick shrubs and small trees started to grow throughout the area, including in the valleys, while wild grasses began to cover the eastern half of National City and Chula Vista, no longer under water.

Five hundred thousand years ago, the flat mesa that would become downtown San Diego was still underwater when an ancient California Grey Whale died there, possibly beached on shallow waters. As oceans levels receded, its remains were buried, not to be uncovered for half a million years.

The extinction of the dinosaurs in the beginning of the Paleogene cleared a path for other life forms to slowly evolve into their places. They started out in Africa as small nocturnal shrew-like creatures, which grew into hominids, then great apes, then early humans, and finally, homo-sapiens. Homo-sapians evolved and spread out across Afro-Eurasia. These humans reached South Asia by about fifty thousand years ago, and reached East Asia by thirty thousand to seventeen thousand years ago. They didn't know that they were migrating across a world. In their perspective, they were simply following the herds of caribou, bison and mammoth that went through their regular migration patterns. They lived where the food lived.

At this point, the Earth's tectonic plates were pretty much where they are today, but the ocean levels still changed the appearance of the land. By about seventeen thousand years ago or about 15,000 BCE, in the area of the world between Alaska and the Siberia called Beringia, the last ice age lowered ocean levels, which allowed these herds, traveling east, to cross the plains of Beringia from Asia onto a whole new continent: North America. By the time this land bridge was swallowed up in the end of the Ice Age, separating the old world from the new, a succession of three waves of humans migrated across the strait. One wave followed the coast line down what would someday be the Provinces of Yukon and British Columbia and the States of Washington and Oregon, adapting to the unique lands and climate of each and making them their new homes. Some migrated further south to the Californias and settled there. Overall, it is estimated that out of the fifty four million natives living in the Americas, ten thousand humans lived in the southern portion of California by the time the Spanish arrived.

By about twelve thousand years ago, some of these people, bringing with them an ancient and little known culture and language, eventually were the first humans in history to discover San Diego: A large coastal harbor full of shrubs, willow trees cactus and cottonwoods, complete with river valleys, distant mountains and cliffs that protected the area from heavy winds and storms. Some humans moved on to Central and South America to become the native empires of those regions. Those empires started out as new agrarian societies that took a wild grass with hard little kernels called "teosinte" and over thousands of years, cultivated it into maize. They also learned to plant, beans, squash and eventually potatoes. The Mixtec were established in southern Mexico first. The Olmec soon followed and the Chavin emerged in modern day Puru. The Maya would come to live in the Yucatan Peninsula, created when an asteroid impacted the area, sixty five million years before. The Paracas were located south of the Chavin, and north of the Olmec, the Zapotec was established. Eventually, they learned how to travel to the Caribbean and the Ciboney appeared in Cuba. Eventually the Olmec, Chavin, and Zapotec cultures disappear. Paracas becomes Nazca, and from the former Zapotec, comes the ancient city of Teotihuacan.

The Maya began to spread in Central America, and new establishments were made in South America, but by 900 CE, the Maya disappeared and so did the Hiari who had taken over Nazca. The Toltec would take over Teotihuacan and after that, the Aztecs. In South America, the Inca began taking over vast regions of land. By the time the Spanish arrived, the Aztecs were in the mist of wars with various other cultures surrounding their empire.

However, a group of humans did decide to stay in future San Diego and enjoy its climate and abundance of food. These paleo-indians named their new home various names according to descriptions of the land such as, "Moc-Nees", which in their language was translated to "Black Land". This is what they called Point Loma, where they would gather clams, mollusks and other forms of abalone. "Cosoy" meant "Drying Out Place" and by then, the once mighty San Diego River had slowed to a trickle and shrank dramatically leaving in its place, a 500 foot inland valley with a relatively muddy flat and hundred foot floodplain, covered in a variety of greenery and wild life. The land that they inhabited was indeed drying out.

I suppose the best way to describe the San Diego natives of this time would be as “stone aged”. They still made their tools out of sticks, stones, shells and bones, and knew little of metals or mining. The slightest flair of a metallic object would fascinate them and they would take rocks with metals that shined, grind them up and use it as face paint. A future archaeologist named Malcolm Jennings Rogers described them as a “scraper maker culture”, meaning a majority of tools they used were simple scrapers. However, for over ten thousand years, this worked well for the natives.

These people lived off of the land as hunters and gatherers. They would mostly eat shellfish, small game, acorns, and seeds. Some of them were completely vegetarian. Because of the abundance of food in the area, they had no need to learn about agriculture like those in the south did. The animals they hunted were bison, rabbits, foxes, snakes, mice, crows, coyotes, frogs, and even cray-fish. To hunt, they made traps and used bows and arrows, clubs, spears, and of course, their bare hands. They refused to hunt or eat some animals for religious reasons, such as dogs, bears, and pigeons. At one point, they may have had horses roaming the area, as horses evolved in the Americas but they were probably hunted to near extinction for food, never realizing the true potential of the horse until generations later.

By around ten thousand years ago, a small group of horses managed to escape North America into Asia, over the same land bridge that brought humans into the Americas. In Asia other humans will learn how to ride and breed them. The horse would go on to help army after army conquer empires throughout human history.

The last of the Columbian Mammoths were still roaming the deserts and coasts during this time, but soon became extinct. One died in future Carlsbad, where the Glen Ridge Apartments are now. Another one died roaming around in future downtown San Diego, directly under the remains of the California Grey Whale that had died two hundred thousand years before, but was now buried under ten feet of sediment. The remains of the mammoth, as well as a treasure trove of abalone, would slowly be buried in twenty more feet of sediment on the grounds where the Thomas Jefferson School of Law now sits.

Winds blowing southeast gathered sediment from La Jolla and Pacific Beach and began to spread it southward, and just like in Crown Point, created a small strip of sand that stretched almost all the way to Point Loma. This strip of land would someday become Mission Beach. The San Diego River used to be higher and wider, and would empty its sediments out into the bay, which was only partially separated by Point Loma. Over time, the land between Point Loma and the mouth of the river became shallower and shallower due to the sediment deposits. The deposit from the San Diego River created a flat plain that once again connected Point Loma to the mainland, splitting the huge bay in two, including a crude version of Mission Bay, which at this time is simply swampy ground. San Diego Bay was so shallow, you couldn’t sail a large ship past Ballast Point, the finger of land sticking out from Point Loma, without getting beached.

Winds blowing northeast gathered silt and mud that traveled west from the Tijuana River, forming an underwater ridge south of Coronado Island. This ridge connected North Island to Coronado through a small strip of land called the Spanish Bight. The ridge follows the western coast of Coronado Island, and connecting it to the mainland through Imperial Beach. As the ocean levels continued to change, these ridges were exposed, giving birth to the Silver Strand, and turning the islands into a peninsula

San Diego’s topography of mountains, canyons, and two bays gave San Diego a microclimate. Normally, cool air comes in from the Pacific and heats up as it moves further inland and over the mountains. As it does, moisture in the air condenses more in the coast than it does inland. This sometimes gives San Diego a thin layer of clouds that will usually cover the coastline area, but dissipates as it moves further inland. Because the temperature is usually cool off of the Pacific coast, tropical storms and hurricanes are a rarity. About ten days out of the year or so, winds will come from the opposite direction, the hot eastern deserts, which brings gusts of hot air to the coast, but usually the climate of San Diego is cool and dry with low humidity, raining less than fifty days out of the year.

By now, the mainland was still much wetter than it is today and was thickly covered with shrubs such as yucca, deer-weed, black-mustard, agave, buckwheat, and sages. However, San Diego at this time is mainly a brown and marshy coastal desert. Trees such as oaks, firs, sycamores, cypress, pinyon pines, cottonwoods, and willow trees dotted the area as well. In fact, there was a forest of pinyon pines in the mountain region. There were no palm trees anywhere except the inland desert area. Out of the 157 species of palm trees that grow in California today, only one species of palm is indigenous to North America: The California Washingtonia, and the closest that it grew is where Anza-Borrego Desert State Park is today. Much of this greenery stretched from the beaches, up the many valleys and into the mountains. The land from Rose Canyon to Point Loma may have once been covered in a thick forest, though evidence suggests that it was covered in the same plants as the rest of the region, though maybe thickly. The rest of the landscape looked pretty barren, with various dry shrubs scattered about. Wild life included rabbits, squirrels, deer, bears, bison, owls, raccoons, skunks, snakes and lizards. Horses and mammoths were long gone. By about 9 thousand years ago – 7000 BCE – San Diego looked pretty close to what it looked like when Spanish settlers first explored it.

Mammoth:
http://www.foxnews.com/story/2009/02/05/mammoth-remains-discovered-at-san-diego-construction-site.html

San Diego Natural History Museum:
http://www.sdnhm.org/

San Diego Geology:
http://www.san-diego.us/san-diego-geology

Salton Sink:
https://en.wikipedia.org/?title=Salton_Sink

The Kumeyaay:
http://www.kumeyaay.info/

Native Civilizations over time:
http://geacron.com/home-en/

California Washingtonia;
https://en.wikipedia.org/wiki/Washingtonia