We are sorry to hear of your situation.
We recommend speaking to the mikveh attendant, or the rabbi/rebbetzin in charge of the mikveh, to discuss your situation. Mikvaot generally change the water regularly or use a filtration system. Furthermore, they generally use chlorine or other chemicals to prevent infection. However, you can request to be the first to immerse after changing the water or on a particular evening after a number of hours of filtration, and confirm that sufficient chlorine has been added to the water.
Otitis externa is generally caused by water left in the ear canal. Be sure to shake out any excess water from the ear canal when you exit the water. You can also speak to your doctor about the possibility of using preventive eardrops (either commercial or homemade) before and after immersing.
In this situation, a single immersion in the mikveh is sufficient; you do not need to dunk multiple times. The bracha should be recited before you immerse.
We hope these tips help improve your situation. If the infections persist, please get back to us.
Please feel free to get back to us with any further questions.
B'Hatzlacha!