Cedar apple rusts can be difficult to treat because there are not many fungicides approved for use on fruit trees. Even if you do have access to approved fungicides, their use can impact the value of your fruit as well as having a negative effect on the pollination of your crops. In most cases, apple farmers would prefer to use an organic treatment for cedar apple rust. However, while ultimately effective, this treatment can be fairly time-consuming to implement on a large scale.
Organic control of cedar apple rust eliminates the fungus by making part of the fungal life cycle impossible to complete. Since you are not likely to want to eliminate the apple aspect of the cycle, the other option is to remove susceptible and infected cedar trees from the area. This prevents the fungus from completing the reproductive stage of its life cycle and eventually eliminates it completely.
There are two ways to target problem trees. You can search by species or by evidence of infection. Juniper and cedar trees that are susceptible to apple cedar rust include eastern and southern red cedars, Rocky Mountain juniper, prostrate junipers and Chinese junipers. Make sure to know the location of these trees in proximity to your orchard for at least half a mile in diameter, even if you elect not to remove them. If you prefer to look for evidence of infection, then look for large, woody, swollen galls on susceptible cedar trees in early spring. They are particularly bloated after a rain.
According to the Ohio State University Extension, you should "eradicate the alternate host within half a mile of your orchard." This means that you will need to cut down trees that represent a threat of infection. If you wait to do this until you spot an infection, you likely will have to deal with at least one season of the problem in your apple orchard as well.
Once you have broken the cycle of cedar apple rust, you will need to keep an eye out for new trees that could be developing the problem on the cedar side of the equation. While you may remove all trees in a half-mile radius, you should still keep an eye on trees farther out in case they might infect closer trees. Remove young problem trees as soon as you spot them. Additionally, rake all plant debris out from under the apple trees and cedar trees at the end of fall and dispose of it in sealed plastic bags or by burning. This will help prevent the fungus from reinfecting either set of trees the following year.
There are organic pesticides available in some states. However, each state's definition of organic sprays is slightly different, and you need to consult with an expert to be sure that you are conforming to organic requirements in your area before you start an organic fungicide treatment. Coppers, sulfurs and limes are considered organic in some areas, and inorganic in others.