I use a vet prescribed shampoo that treats fungal and microbial infections. We used to soak my dogs feet in it because he would get yeast infections under his nail beds. That helped a lot.
However, the licking at the paws is usually associates with an enviromental allegry and given the fact that he is in the water so much, there is a chance that something either in the water or somewhere else in the environment is causing the reaction. I would suggest keeping him away from the water and excersizing him in another way until you can get to a dermatologist and see if it helps.
