Yes. Flushing unused medications down the toilet can kill the bacteria in the septic system. Contact your local county health department to see if they offer programs to collect and dispose of unused medications. Flushing unused medications down the toilet may also increase the risk of drinking water contamination. To limit the possible harm to the septic system and possible contamination of drinking water, it is best to prevent medications from entering the septic system. Since human waste can contain certain levels of medications, it would be difficult to prevent all meds from entering the septic system. If someone in the home is using a lot of prescription medications, (especially with individuals on chemotherapy regimens) the use of bacterial additives may be helpful in maintaining sufficient bacteria in the septic system.