This "sea" is actually a shallow, saline lake in California's Imperial and Coachella valleys that sits right on the San Andreas Fault. It's fed by the New, Whitewater and Alamo Rivers along with agricultural runoff, drainage systems and creeks.
For millions of years, the Colorado River flowed into valleys, depositing soil and creating fertile farmland. The soil buildup constantly changed the river's course. For thousands of years, the river has flowed both into and out of the valley, alternatively turning the area into a freshwater lake, an increasingly saline lake and a dry desert basin.
The filling cycle lasts about 500 years before repeating; the latest cycle occurred around 1600-1700 C.E., according to the Native Americans who spoke to the first settlers.