I don't know if there is anything you can do...it often depends on the leather. Water stains tend to be pretty hard to get rid of especially on light coloured or poorly tanned leather. When shoes get that wet, residual tanning compounds, superfluous dye stuff, and even salts get deposited in greater concentrations in just the same way that the tide leaves a line of spin drift and detritus on the beach as it recedes. One thing you can try if you are game...get your shoes entirely wet again. Fill a bucket with warm water and chuck them in there and let them sit say, four hours, completely submerged. Pull them out, shake or towel off the excess water and cover them with a liberal wash of Lexol (in the tan container). If you have R.M. Williams Saddle Dressing or anything like it, coat the leather with that, as well. Both of these products will slow down the drying until the moisture can even itself out. The R.M. Williams is actually a little better at this than the Lexol but several coating of Lexol may compensate. Turn the shoes upside down and allow to dry slowly, applying more Lexol as necessary. You might even rotate the shoesupside down, on their sides, right-side up, etc.--if they seem to be drying too fast on one side of the shoe or the other. If the shoe has a chance to dry slowly and evenly, sometimes...sometimes...those residual chemicals and dye stuffs can be redistributed. When thoroughly dry, recoat everything, inside and out with Lexol and polish. Now for the disclaimer, if your shoes are gemmed or have paper insoles, etc., etc., they may be damaged by this treatment (if they are not already damaged). But if they are well made shoes, and you assiduously recondition them, you should not damage them and you may get them back to an even, or very nearly even, colour. Second discalimer...again with the tannage and the quality of the leather...this is not guaranteed to work and it may not be for the faint of heart. But when it works it's dern near a miracle.