A method and system are disclosed for detecting the presence of a gas in a pump chamber of a pumping system. The methods, and systems employing the methods, involve isolating a pump chamber from its surroundings, for example by closing an inlet and outlet valve on lines to and from the chamber, and determining the volume of the pump chamber with a force applied to a moveable or flexible surface of the pump chamber. The volume of the pump chamber is then redetermined in a similar fashion but with a second, different level of force applied to the surface of the pump chamber. The volumes thus determined can then be compared to detect the presence of a gas in the pump chamber.