Last week, Hurricane Sandy made landfall in Atlantic City, NJ. Atlantic County and Cape May County (see map) were under mandatory evacuation orders. Cape May County is home to the city of Cape May and the first desalination plant in Northeastern U.S. Here is a little primer on Cape May from Vedachalam and Riha (2012):
Cape May (38°56′24″N 74°54′19″W) is a coastal town on the southern tip of New Jersey and is surrounded by the sea on three sides. Although the population of the town is only 7000 during much of the year, the summer population swells to around 45,000. Cape May has historically depended on the Cohansey Aquifer for its water supply
Although there were no reports of damage to the desalination plant, this is an issue worth considering. All the desalination plants, for obvious reasons, are located either on the coast or in brackish waters close to the coast. Large storms like Sandy can potentially knock off these plants (even temporarily) and render nearby regions water-deficient in the short-term. Another long-term concern would be the safety of these plants due to the rise in the sea levels. It is not clear if the 3 desalination projects in the Northeast considered the storm surges in their construction plans, but new/forthcoming* projects will have to do so.
*I think the Haverstraw plant in Rockland County, NY has included some climate change scenarios in its DEIS.