For deep cracks in wood, skip the standard wood putty. Instead, use a two-part wood epoxy. Unlike putty, epoxy bonds to the wood fibers and does not shrink. Clean out any rot with a screwdriver. Apply a wood hardener to the area.

If you notice water stains on the drywall inside your home directly beneath the window, the leak has likely bypassed the sill and entered the wall cavity. At this point, simple patching won't suffice. A professional contractor can assess if there is hidden rot in the wall studs or if the window flashing was installed incorrectly.