I have find this on many wheels I've had in my life and found that the water marks are caused BY the "Wonder wheels" as it contains acids of sorts I've been told and so basically it strips the wheels laquer to the paint then the water marks sticks like brown stuff on a blanket...
in the famous words of Iain.....
Prevention is the cure.
You will have to use a car polish to rid the water marks, using the likes of Megiuars Scatch X "Very lighty" on the wheel all over to rid the tar marks, water marks and etc... then once you have done that, cover them in a high grade wax like Meg's #16 hard wax or any hard wearing wax, a few coats of this will prevent the water etching into the alloy, well long enough between washes, so all it means that the waxing continues to wheels too, when u wash the car...
Thats the best way i have found, and i tell u I've tried pretty much everything on the market, it wasnt till i learnt on here that they use acids and etc, i changed my ways and well now my wheels are EASY to clean now...
P.S little note, allow the wax to cure overnight if you can makes it harder wearing i do two in one day, then 2nd layer overnight then next morning i buff it off...and also make sure u have a seperate buffing cloth and application pad to do the wheels, never use the same one u use on the car... common sense thou that!
Hope that explains abit....
(Iain hows that yoda? lol )