My boyfriend many years back had toe fungus. He had had it since he was a kid. We lived on Cumberland Island off the coast of Georgia for one summer. We were barefoot and in the ocean all the time. After a few weeks he started to notice that the fungus was going away. It went away entirely and, as far as I know, (I haven't seen him in some time) it never came back.
Short of going to the ocean, maybe try soaking in salt water. I have also heard of people using vinegar for this and exema - which is a fungus too (I think?)