Desal can be problematic for three reasons.
(1) First, it uses a lot of power, and if that power isn't produced sustainably, you've got more emissions, etc.
(2) Second, there are things living in the water that gets sucked into the plant. Much of it gets caught by filters before it gets into the plant. Some things die on, or are injured by, the filters; other things die because they passed by the filter.
(3) Third, the plant discharges large quantities of brine back into the ocean. For every two gallons of seawater taken in, the plant produces one gallon of desalinated water and one gallon of brackish water. That brine changes the salinity near the discharge pipe(s), affecting the local biosphere.
These effects should be compared to the effect of other sources of potable water, such as diverting stream flows, which also have negative consequences. Of course, as with energy conservation, the cheapest and most sustainable gallon of water is the gallon that didn't get used.