I still don't quite get what you're saying where the window is. Cause there's no such thing as a ceiling window, besides a skylight, light tunnel or for commercial applications a glass or plexiglass type of roof panel.
A basic window doesn't explain much. Is it a vinyl, wood or aluminum framed window? Are they single, double or triple paned? Is the window operable (sliding, single hung, fixed, casement...)?
Do you mean it's a window just below the ceiling and built into the wall? How old are the windows? If the seal is broken around the glass panel u can try to repair it but it won't be very durable in my opinion.
If it's a newer window, any gas between the window panes has probably escaped which you probably don't care too much since it appears your main concern is water seeping in.
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