It may not be water marks but a harsh cleaner. Most bike grime cleaners, such as much off, fuchs off and pro clean are fine, but be carefull not to leave them on to long. More powerfull cleaners such as dirt bike cleaners or truck wash are to harsh and will discolour the laquer or painwork. I should know my swing arm has suffered !!
Don't polish too much or you will go through the top anodized coat, most of these are caused by cleaners being left too long as MRD said above, water itself will not mark it.
Christ, I've had soap stain the frame when I've not washed it off properly, or rain leave a dirt mark but i've never seen this (thankgod). A dollop of T-cut has always shifted it.
might have to polish through the coating down to the metal and then get the lacquer re done. will let you know if i find a less drastic answer. cheers.