Bacterial conjunctivitis treatment. Bacterial conjunctivitis typically affects only one eye and is usually characterized by a yellow discharge. Once your doctor suspects bacterial conjunctivitis, he or she will take a sample of the discharge from the eye which is then tested to determine the type of bacteria. Generally, bacterial conjunctivitis will clear on their own in about 1-2 weeks without needing any medication. However, to help speed up healing, or if the bacteria is related to an STD, an antibiotic will be prescribed in the form of eye drops or ointment. You will be required to apply the antibiotic to the inside of your eyelids, usually up to 4 times a day. Assuming you apply your medication correctly, according to instructions, you should start to see your eyes clearing up pretty quickly.