I borrowed this from Pete Ramey's site. Pete has rehabbed hundreds of horses.
Fungus is usually primary with a secondary bacterial infection eating tissue. Whatever you use, don’t use something that kills live tissue. While Kopertox is traditionally used to treat thrush, it is a nasty poison, both for us and the horses, and the environment. It also kills live tissue, providing more "food" for the invading organisms. I personally have had very good results with a product called White Lightening from Grand Circuit. These products should be used when the thrush is invasive and wide spread. Lysol Concentrate – All Purpose, any color, can also be used. Mix according to directions at 2 oz per gallon. Do not make it any stronger. Do 30 minute soaks three times per week. EasyCare Soaker boots work very nicely for soaking.
For deep central sulcus thrush ( that crevice I talked about above), use what I call "Ramey Goo". This is a 50/50 combination of Triple Antibiotic Ointment and 1% Clotrimazole Athletes Foot Cream that Pete Ramey came up with and has had much success with. (Generic Brand is fine) I buy 1 oz tubes of each, mix them together in a small container and then use a small spatula to put some in a 60cc catheter tip syringe. The easiest way to get the goop out of the tubes is to cut off the bottom of the tube and squeeze it out rather than trying to squeeze it out the tip of the tube. When you use two 1 oz tubes, you end up with 2 oz's of cream. Only put 1/2 to 1 oz of the cream in the syringe at a time or you won't be able to hold the syringe in one hand and plunge the "goo" into the crevice.
Do not tolerate deep crevices in the sulcus! This is not normal. It’s not so much about the “stuff” we treat it with as is the stimulation required for healing. Every pressure and release action stimulates growth. Foam rubber (like using boots with pads and exercising the horse) and 4” deep pea gravel work wonders. If you beat thrush in the sulcus, you’ll beat it everywhere else.