Here's how they do it at MRT stations in Bangkok, a city prone to torrential rain and widespread flooding: just put the entrances above flood level.
Source
On Front Street, where the land slopes away at York and Bay streets (and therefore water is not likely to rise more than a couple centimetres on the sidewalk), a single step up should do the trick. At the moat entrances along York and Bay Streets, grilles with cisterns below may be needed assuming they don't want to lose barrier-free access.
42