According to German Town Vet, there are a few causes of brown gunk inside a dog’s ears: Excessive Earwax. This is the most likely reason for the brown substance in a dog’s ears. Earwax production is normal and nothing to be concerned about. However, too much wax can lead to an ear infection, so watch out for other signs, such as scratching and rubbing of the ears, frequent head shaking, or redness and swelling. Fungal Ear Infection. A dark brown discharge with a pungent, musty odor most likely indicates a fungal or yeast infection. This is often caused by excessive moisture build-up in the ears. Ear mites. Crusty, blackish-brown build-up resembling coffee grounds in a dog’s ears is a sign of ear mites. Ear mites are tiny insects that can make dog’s ears their home. Left untreated, ear mites could make a pet lose its hearing. Outer Ear Infection. Also known as otitis externa, an outer ear infection is characterized by a yellow, waxy, or reddish-brown discharge. Such infections can be caused by allergies, polyps, or any of the above problems.