There are several layers to prevention. The first starts with making sure your horse's environment is free (or mostly free) of his own manure and urine build up. I know it's not possible to have completely clean pastures and paddocks all the time, but if there is an area that the horses like to hang out at lot ie. run-in shelters or near a water trough that is collecting manure and urine, your horses will be standing in it and that is a breeding ground for thrush. Be sure to clean those areas regularly and make sure there is proper drainage so that the urine can run off.
A lot of people assume that muddy environments are also going to cause thrush and this is only partly true. Horses with compromised hooves/immune systems or with no where to get out of the mud will likely have thrush issues but mud itself does not cause it. Healthy hooves with at least one area that is dry in a turn out area should be able to tolerate muddy seasons in their living area.
Having a proper diet is also a factor. You hear natural hoof care proponents commenting (or obsessing over) your horse's diet a lot and the reason is that hoof quality is a by product of it. Just like humans cannot exercise their way out of bad eating habits, we trimmers cannot trim your horse's hooves out of a poor diet. Excess sugar and starch can be inflammatory to your horse's entire system making it more suseptable to infection and that's what thrush is! Also, making sure your horse is getting the proper vitamin and mineral balance is crutial and this can be done by testing all of the sources of food (grain, grass, forage, etc) your horse has access to and having it evaluated.
Once you have all of your preventative measures in place, you can be sure that your treatment measures won't be erased! Here is a list of treatment options that I recommend rotating through depending on your situation. I suggest using several different methods because, unless you take a culture swab of the area, you won't know exactly what you are treating (fungal or bacterial) so I find it's best to find whats best for your horse by rotating. Always ask your own trimmer/farrier which they recommend for your horse's particular situation. For most treatment plans, daily or twice daily applications usually get the fastest and most positive results!
Apple Cider Vinegar: 1/2 and 1/2 either shallow soaks or in a spray bottle applied once weekly as a preventative measure. Most of us already have this on hand!
"Pete's Goo" - can be made yourself! equal parts clotrimizol, triple antibiotic ointment +pain relief and diaper rash ointment
Cow Mastitis medication - Tomorrow, Today or Albadry are some of the names this goes by (works very well for deep sulcus infections) Can be ordered or found at most farm supply stores in the bovine section.
Hoof Powder- I make my own blend of a powder-like treatment. Works very well in wet environments and used in hoof boots to help keep the moisture down! Email me to order some :)
Red Horse Products - Artimud or Field Paste. Can be ordered through farrier supply companies.
*Note - I avoid any products that contain formadahyde or that are potentially causitic! Thrush infections can be very painful to your horse so you don't want to use anything on a potential wound that would hurt or that will kill good tissue along with the bad.
Hopefully these preventative measures and treatment options will help to keep your horses fungus free!