Systems and methods for disinfecting medical instruments are provided. In one embodiment, a system can include a hood to provide a clean zone, a chamber to dispose within the clean zone, and an ultrasonicator. More specifically, the chamber can include a volume and can be configured to retain a fluid and receive medical instruments. The chamber can also include a portal through which fluids enter or leave the chamber. The ultrasonicator can be used to sonicate the volume when the fluid is present. A related method of disinfecting medical instruments can be accomplished using the systems of the present disclosure.