To get rid of brown yeast in a dog's ears, the dog may have an ear infection, which can be a result of allergies, mites, polyps, overproduction of ear wax, excessive bathing or swimming, or other problems. Treating an external ear infection may require an antibiotic as well as an antifungal lotion, oral medication, an ear-cleaning solution, or an ear-drying solution. If your vet prescribes ear drops to clear up your dog's ear discharge, you may need to apply them for a few weeks. Make sure you follow the veterinarian’s directions: Cleaning the ear canal may not optimize certain medications, and others may require more frequent dosing. If your dog swims a lot or tends to get ear infections, ask your vet about products that dry out the ear canal and prevent the growth of bacteria and yeast. Keep the inside of your dog's ears clean by removing visible dirt with a cotton ball soaked with a canine ear cleaning solution. A waxy, yellow, or reddish-brown ear discharge can also be a sign your dog has an ear infection. Dogs with drooping ears are more prone to ear problems, but any dog can have ear mites, develop an infection, or get an irritant like burrs or seeds stuck in their ears.