A bubble trap assembly for critical bioprocess applications. The assembly includes a disposable liner including a gas port disposed on a top of the liner, and two fluid ports disposed on the bottom of the liner. The fluid ports coupled in-line to the critical bioprocess application. A rigid vessel is included for housing the liner. The liner being sized to substantially conform to a shape of the inside of the vessel. The vessel includes an upper aperture for aligning with the gas port and a bottom opening opposed to the upper aperture. A bottom cap is included, removeably secured to the vessel and closing the bottom opening. The bottom cap together with the vessel substantially enclosing the liner. The bottom cap includes two lower apertures for aligning with the fluid ports. The bottom cap being formed by two cap portions capable of being separated.