Hmmmm.... resist magicka? If not, I'd recommend cheating
Since you're modding anyway, I'd create a ring (I always pick rings, they weigh less than amulets) with a script attached,
if ( OnPCEquip == 1 )
SetWaterWalking, 0
endif
I've never written a script that set a spell, so I might have written that in bad syntax... it could be SetWaterWalking == 0 or SetWaterWalking to 0, my guess is the first but one of the 3 should work and solve your problem.
Then, through the console, add the item to your player's inventory
player->AddItem "My Ring of Sinking" 1
Also, it occurred to me after I wrote the above, you might want to try a remove spell or remove spell effects, so
if ( OnPCEquip == 1 )
Player->RemoveSpell, "Water Walking"
endif
LOL please let me know if any of these work, I might need to use something like that some day...