A dental waste containment system having a treatment stage to reduce the contaminant levels of the stored fluid. The treatment stage may include a settling canister disposed before the fluid storage reservoir to remove and contain at least some solid contaminants from the fluid waste before the fluid waste is moved into storage. The system may include a bypass subcircuit to allow fluid waste to selectively bypass the treatment stage. The present invention also provides a method of collecting, containing and transporting dental waste that includes separate containment of solid and fluid dental waste. The method includes at least partial separation and containment of solid contaminants in the treatment stage before the fluid dental waste is moved into separate storage. The accumulated fluid dental waste and accumulated solid waste may be separately collected from the system and separately transported to a remote facility for treatment, reclamation and/or disposal.