Simple: cost

As long as it is cheaper to exploit an existing clean water source than to spend the energy, and invest in the massive and in some cases unproven tech and engineering infrastructure to build desalination plants, then that's what will happen.

It's unfortunate, because the cost to future generations, or the biosphere doesn't calculate into our current economic system, and most of the commercial infrastructure is aligned against re-calibration of that kind, because it would cost them dearly.