To understand why water doesn't bother the batteries or the motor in an electric car, first consider the fact that every car you've ever driven has had an electrical system. It operated at much lower voltages, used a different kind of battery and served a different purpose from the system in a hybrid car, but the principle is the same. All cars have batteries and electric systems, yet they don't short out or shock anyone in the rain. Even if you get water on the battery terminals, it generally just causes corrosion, not an immediate catastrophic effect. In fact, in several models, notably certain Chrysler vehicles, the 12-volt battery is mounted behind the front tire, near the bottom of the car, where it is frequently exposed to water and other road debris.
Hybrid and electric car batteries are a bit different. They're larger, have more cells and contain nickel-metal hydride instead of lead-acid. Some batteries are made using lithium-ion technology; however, lithium-ion batteries are not very common in cars -- not yet, anyway. In the most typical configuration, the batteries are placed behind the rear seat, sometimes in an enclosed section near the trunk. In the Toyota Highlander SUV Hybrid, the battery pack is underneath the rear seat, bolted to a structural cross member. In early Toyota Prius models, the battery pack was mounted flush to the back of the rear seat. The point is, in a typical electric or hybrid car, the battery pack is usually nowhere near an area where it could get splashed with water from the road.
On the other hand, in some designs the battery pack is mounted near the bottom of the car. What then? Hybrid vehicles manufactured in the United States have a battery pack encased in a sealed metal shell. The shell is electrically isolated from current flowing from the batteries and usually covered in carpet or with an interior panel. Even though the shell is metal, if it does get wet, it's treated to resist corrosion.
In the event that water does actually get inside the shell, there's still not much to worry about. The nickel-metal hydride batteries used in current hybrids and electric cars are maintenance-free sealed cells, so nothing gets in or out. The chemicals inside are designed to form a gel, so they won't spill even if the batteries are ruptured in a crash. Under normal operating conditions, it's pretty much impossible for water to come into contact with the batteries themselves. The high-voltage lines that carry the current are similarly protected and insulated.
The bottom line -- don't worry about dodging puddles in your Prius.
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