You live in a hard water area?
I get some water marks but usually come out with the chamois leather.
Rub harder 
My god do not rub hard with a chamois leather

You'll scratch the paint work. Dry your car off with a microfibre drying towel then use a detailing spray, I like to use Meguairs ulimate detailing spray and a microfibre. Spray it on and work it over the area with the microfibre, then with a dry microfibre buff the area to leave a shiny non water marked area

Also its best not to wash your car in the sun. I normally wait til its going down or do it early in the morning.