Regular GPS? Tom Tom?

What type is it? My assumption is a regular car navigator or motorcycle type of GPS. If I'm not mistaken, I don't think TomTom make handheld unit like Garmin or Megellan.

If that is true, then the motorcycle unit are already water proof. You can try using a map bag that strap on to your handle bar and put the unit it that. The bag has a clear plastic face for placing a map and since most GPS are pressure touch screen, you can still activate the menu.
Here is a link from REI
http://www.rei.com/product/780457

Your other choice is to have a place like Tap Plastic here in the west coast or whoever acrylic store in your area to custom make a 1/8" Acrylic box for your unit. You can make it with six side but leave one side (left or right) that has a slot so that you can put theunit in it or your hand in it to select your menu.