Um, some of the responses in this thread are worrisome.
What you REALLY need to do is to work in steps. Start with a mixture of white vinegar and water with a rag. See if you can't get them off. If not, you have water deposits, not water spots. What happens here is that since when rain falls it isn't truly pure because of pollution, the water evaporates and the contaminants don't stick to the glass, they embed themselves into the glass. You need to get an aggressive claybar from a detailing shop or online, and go to work on the windows. If THAT doesn't work, then try a GLASS polish via random orbit buffer. This will polish them down. If that doesn't work, step up the glass polish to something more aggressive and use a rotary buffer. Mind you, the rotary buffer can leave hazing which you will then need to remove with the random orbit, or a finer polish. If none of this works (I can't imagine that it won't), then your only solution is to get a new window frankly. Wetsanding and steel wool for people who don't detail is a completely retarded solution. You'll just wind up scratching your glass to hell and back.