electrical shorted out after rain leaked into closed car

Since California has been in drought, heavy rain hasn't happened lately, but recent storms ended up with an inch of water collecting on floor of passenger and driver. First incident had engine battery (not hybrid) dying and replacement was made since diagnostics from AAA show no voltage. Second incident of rain with rain resulted in total short out of electrical. No windows were open, no apparent breaches in body. Suggestions have been drainage of moonroof might be involved but not water anywhere except floor.