Animal Waste Put in Garbage Cart Pick It Up Many pathogens in pet waste are harmful to humans and other animals. When left on the ground, pathogens like Salmonella or E. coli can leach into water systems. Be sure to pick up pet waste at all times. Don't Compost Waste Don’t place pet waste in commercial or backyard composting, even if you are using compostable bags. Doing so transmits diseases and invites animals to rummage through any backyard compost pile. Never Flush Cat Waste Down the Drain Cat waste can possess especially toxic pathogens. The best way to dispose of pet waste is to bag it and throw it away, in order to reduce polluting streams and rivers.