The vehicles have enough information to make the determination. Ground data is available in the point cloud and usually labeled as such. Water sometimes shows up in point clouds, sometimes it doesn't depending on conditions and wavelength.

If the apparent road surface is higher than the mapped ground surface, probably a puddle. If your point cloud has a big hole, also probably a puddle.

This assumes you aren't doing ground plane removal, of course. But it's quite likely that Waymo is using a heavily ML approach these days, and I can imagine the poor thing getting very confused if it's not an explicit training goal.