Desalination is a plausible solution for water for consumer use--that is, urban and suburban locations.
It is not a very plausible solution for agricultural use-- too expensive.
Actually, there are a number of issues with desalination as it presently exists. The cost of plant construction and operations puts the cost of water supply at roughly triple that of traditional methods.
Exactly. That's why it's not a plausible solution for agricultural use. If your application is to take water and spray it on the ground, yes, it needs to be cheap.
For urban and suburban use-- well, given the rents, and the cost of housing, in San Diego (not even to mention San Francisco!)-- the cost of water just isn't a factor. You could triple it and not notice.
They also depend on fossil fuels and thus contribute to greenhouse gasses. They produce brine and boron contaminants that can not easily be disposed of on either land or sea without potentially significant impact of the wildlife exposed to them.
Those are engineering problems.