A toenail fungus infection is caused by the same fungus that is responsible for an athlete's foot infection. Often, a toenail fungus infection is caused by an untreated athlete's foot infection that has spread to the toenails. Fungus in the toenails can be tricky to treat because the fungus is protected underneath the toenail. If treatment is ended too early, before all the fungus is killed, the infection can come back quickly. There are several natural remedies available to treat toenail fungus. Natural treatments should be continued for at least two weeks after all signs of the fungus infection is gone.