You could maybe use short-wave infrared cameras combined with ground penetrating radar, but it'll get real expensive so probably not commercially viable.
I think the only "good" solution is to have the car be overly paranoid, and if it detects water on the roadway that's bigger than some arbitrary diameter (to rule out mud puddles), then the car has to assume its a flood, stop, and escalate to a human or change the route.
Alternatively, just don't run Waymo operations during flood/flash flood warnings. Maybe we as a society need to top forcing everything to still operate normally during natural disasters. It's OK to shut things down when safety calls for it, and that applies to human drivers too. If areas are flooding, stay home.