Water stains on window sills can be a source of anxiety for home buyers, and it's the home inspector's job to help determine if the stains are the sign of a major problem or not.
There are three common causes of water stains on windows:
1. Leaving the windows open.
The windows get left open, and water pours in through the window during a rain storm. This type of staining will often leave fairly uniform water staining across the window sill.

2. Condensation.
If it's a wood window, you'll see stains at the corners of the window sashes and the window sills if the stains are caused by condensation. You'll also find the worst stains on the windows that are most likely to be damp, such as in bathrooms or bedrooms just outside the bathrooms. The windows at the north side of the house will be worse than windows on the south side.
3. Leaking windows.
If water is actually leaking in to the house around the opening for the window at the siding, this will typically show up as staining at the corners of the window sills. The photo below left shows what a window sill may look like with minor water leakage in to the wall; the photo below right shows a window sill with major damage from water leakage. A home inspector could use a moisture meter to help determine if the stains are currently damp.