http://www.scientificamerican.com/article/the-impacts-of-rel...
http://www.scientificamerican.com/article/the-impacts-of-rel...
It's what you'd expect, in fact. The state of California (if my back of envelope calculations are correct) uses in total about 66 cubic kilometres of water each year.
If you produced California's entire water supply by desalination, this would be akin to removing 1/10,000,000 of the Pacific's water every year. It's a miniscule amount, and is of order of magnitude the same as not letting the Colorado reach the ocean.
Summary: Can be bad, but effects localised to tens of metres when done properly (i.e good flushing).
"It must be noted that a large proportion of the published work is descriptive and provides little quantitative data that we could assess independently. Many of the monitoring studies lacked sufficient detail with respect to study design and statistical analyses, making conclusive interpretation of results difficult."
"It is clear that greater clarity and improved methodologies are required in the assessment of the ecological impacts of desalination"