Most homes and businesses have thermal pane windows that have a sealed air barrier between the two panes. Less common are single paned windows. A simple way to find out if the stain can be removed or not is to lick your finger and apply it to the stained area. If the area temporarily appears clear on the wetted area, the stain is most likely fixable. Unfortunately, if the stains are located between the two window panes, they usually cannot be removed.
Various factors can cause stains on windows, including: sprinkler systems, oxidization, hard water, salt spray and rust. Most of these stains can be prevented by regularly having your windows cleaning (at least yearly). Regular window cleanings also help prevent your glass from degrading due to hard water, oxidization, pollutants and other factors.
In Santa Fe we tend to have hard water due to high mineral deposits. Hard water stains can occur on windows from rain water or sprinkler systems. It is best to check your irrigation system to ensure that any spray from your sprinkler system is not hitting your windows. These hard water stains can be treated by a professional window cleaning crew.
A protective coating can be applied to glass to prevent repeat staining. Products such as these create a molecular barrier to prevent against new stains, as well as repelling dirt and preventing incidental scratches.