A catheter pump system is disclosed. The catheter pump system can include a shaft assembly and an impeller coupled with a distal portion of the shaft assembly. The catheter pump system can include a motor assembly, the motor assembly comprising a chamber and a shaft-driving portion disposed in the chamber. The shaft-driving portion can be configured to impart rotation to the impeller through the shaft assembly. The chamber can be filled with a gas that at least partially surrounds the shaft-driving portion. A fluid pathway can convey fluid proximally during operation of the catheter pump system. A bypass pathway can be in fluid communication with the fluid pathway, the bypass pathway configured to direct at least a portion of the fluid to bypass the chamber.