I might be wrong, but aside from a "spring fed" lake that can withstand a drought, most of the other lakes are either made from low basins along a river's path, as a result of tectonics, or created artificially by animals like a beaver and us.

Farms, golf courses, other businesses, and homes pump far more water out of the region's aquifer than is restored by normal rainfall, so the Coachella Valley Water District pipes in water from the Colorado River and, basically, pours it into the sand at the high end of the 15-mile-long valley.

This water then percolates through the sandy soil down the valley; it's retrieved through local wells. One advantage to delivering the water through the aquifer is that it avoids loss through evaporation.

The Coachella Valley’s groundwater basin can be imagined as a tilted bathtub filled with sand and gravel and topped with a layer of clay; water fills the spaces under the clay and in between the sand and gravel. --Coachella Valley Water District

This system works because:

• There is a (relatively) plentiful external source of water.
• The local geology allows water to flow.
• The replenishment is largely powered and directed by gravity, which makes it cheap and avoids having to pump water into a system that already has liquid in it and having to worry about whether the water is going where you want.

This Stanford University project talks about the opportunities and challenges for aquifer recharge projects.