Abstract: Aspects are provided for pumps and methods and systems for controlling pumps based on a bubble sensor. A pump system includes a drive motor, a pump head that receives tubing, and a controller configured to control a rotation of the drive motor to move a liquid within the tubing from an inlet to an outlet. The bubble sensor is coupled to the tubing downstream from the outlet and configured to send a signal to the controller in response to presence of a gas bubble within the tubing. The controller is configured to: determine a quantity of bubbles detected based on the signal; determine an alert in response to the quantity of bubbles detected exceeding a threshold; and stop the drive motor after a safe operating time from the alert. The threshold and the safe operating time are based, at least in part, on a characteristic of the tubing.