Question on Cleaning/Washing/Waxing

Ok I've had my malibu for about 2 years now. I've typically washed it once a week or two weeks except during the winter months. I have waxed it twice and just general detailing but after washing it a couple months ago I felt along the hood and it was really rough feeling so I thought i would clay bar and wax it again.. Well we finally get a nice day to do so and I wash and detail then clay bar it.. It feels so smooth now but it looks like there is dried up embedded water spots in the paint on the hood.. >.< I always hand dry the car when I get done washing and the clay bar did smooth the surface but it couldnt get the water marks out..

Is there anything out there that might work for this? >.<