Yes, most often, if you have comprehensive coverage. Your car is covered for just about anything that is unintentional with comprehensive coverage, so flooding should not be a problem.
Interestingly, even if your car is in your garage, your house is most likely not covered for floods, as that is carved out of normal home insurance policies, but your car would be. This may be important to clarify during storms and house flooding events.
All this is only the case if you have comprehensive coverage. If you only have the legal minimums, then you would most likely not be covered for damage to your own car, no matter what the source.