It's not uncommon for showers to have windows. It's also not uncommon for those windows to experience water damage. The water damage is caused by improperly waterproofed windows. While silicone may seem like a quick and easy fix, it's not enough for the long haul. Although rainwater can beat down on the outside of a window, there are a few steps that must be carried out to ensure that it is protected from the inside.
Run cement board across the shower area on the same side as the window jamb. Use a healthy dose of silicone caulking between the cement board and the jamb. Do not skimp on the quality of caulking. In this case, cheaper is rarely better. Be sure to use a permanent caulking that is specifically for baths.
Install a waterproof membrane that can be wrapped around the window joint and the wooden jamb. Use a latex-modified thin-set to attach the membrane to the jamb and follow manufacturer's instructions for drying.
Install a pitched windowsill made of a water-impervious material, such as acrylic polymer. A pitched sill will let the water that hits the window drain back into the tub instead of laying stagnant. To created a pitch, build up a few layers of latex-modified thin-set closest to the glass. Keep the thin-set thicker than usual for ease of layering. If your shower is tiled, tile over top of the sill for a unified look.
Add additional caulking to the entire window. Anywhere in which two planes intersect will need to be covered. Check the window periodically for leaks and cracks.