Specifically groundwater use with poor drainage leads to salt accumulation over time as the water evaporates and the trace amounts of salt present in the "fresh" water are left behind.
The central valley accounts for 1% of US farmland by area and 8% of US agriculture by revenue. Whatever they're doing wrong, they're also doing something right.
What they're doing is raising exotic cash crops instead of huge fields corn and soybeans. The climate allows them to grow crops that would not survive midwestern winters, like almonds.