Klaus Jacob had been warning New York City for a decade that a hurricane like Sandy barreling in from the east could flood downtown Manhattan and coastal New Jersey. Most recently, he and other scientists published a big 2011 report detailing the threat and recommending ways of protecting the region against storm surges. Jacob felt Sandy's wrath firsthand, too—his house in Piermont, N.Y., on the enormous Hudson River about 25 kilometers north of Manhattan, was flooded with 60 centimeters (two feet) of water. He had already raised his home as much as local building codes would allow, but clearly that was not enough. Jacob, a seismologist and specialist in disaster risk management at Columbia University's Lamont–Doherty Earth Observatory in Palisades, N.Y., graciously took a brief break from his hectic day of shucking out mud from his ruined home (see video by his colleague) to explain to Scientific American what coastal cities and townships must do to prepare for more destruction from rising sea levels and storm surges.

[An edited transcript of the interview follows.]

City and state leaders on the U.S. east coast are suddenly talking about putting barriers outside of New York City and other places. Will those work?

Barriers are not sustainable structures for more than 100 years, so they will not be sufficient for, say, 500 years of sea-level rise. Barriers can work, but you should only build barriers if you have an exit strategy for them [a plan to update them]. Hurricane Katrina in New Orleans overcame man-made barriers because the city kept subsiding and the sea had risen after the levies and walls went up. You have to take action behind the barriers to prepare for their obsolescence—before you design and build them.

Is that what is happening in the Netherlands now?

The Dutch built their barriers [beginning in the 1950s] for a one-in-10,000-year flood. But now that is approaching one in 1,000 because of sea-level rise. By the end of this century the barriers will only be good for a one-in-100-year storm. At that point, with sea level at one or one and a half meters higher, an annual storm could equate to a thousand-year storm. They are rethinking what they must do.

Would it be better for cities to alter their building and transportation infrastructure instead?

They need to do both. But I think it is better to focus on land use and municipal planning. Most immediately, buildings on low ground should pull all their systems out of basements and put them on higher floors. Tall buildings should put their systems on the 10th floor. Let the lower level be a parking garage or something. Then waterproof the basement and low floors. In New York City transportation systems like subways have to close all ventilation grates at the street level and find other ways to vent. Gates are needed for subway entrances—or the entrances should be redesigned; in Taipei, for example, at some station you have to walk up from street level to enter before you can walk down below street level into the subway.

What about retreating from the coast?

Yes, we should retreat in certain low-lying areas. Insurance companies will not insure any property that is at a dangerous elevation. National flood insurance should also be revised; it is almost a hoax right now.

It sounds like a number of issues have to be addressed at the same time. Can cities perhaps share solutions?

Every location needs a customized plan. There are many things a city can do, including retreating. But we also need to change land use up and down the entire U.S. east coast. We must overcome "municipal home rule" by towns, so that states or regions can implement sensible land-use policies. That will be a huge political battle, but home rule can make larger solutions almost impossible.