Apple applied for a patent for a method of color correction on underwater pictures, which is what inspired those rumors, but at this time no one knows whether any future iPhone will be waterproof. We'll have to wait and see.
A couple of things that support this rumor are the other rumors that the new phone will not have a standard headphone jack, and that the home button will be pressure sensitive. Those are changes that you would make if you were trying to make your phone waterproof, so it feeds the rumors, but we still just don't know for certain.
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