Thrombectomy catheter and pump assemblies for controlling a flow of effluent from a thrombectomy catheter. An illustrative assembly may a thrombectomy catheter, a pump, a connection manifold assembly positioned between the thrombectomy catheter and the pump, an effluent return tube fluidly coupled to the thrombectomy catheter and the connection manifold assembly, an effluent collection bag, an effluent waste tube fluidly coupled to the connection manifold assembly and the effluent waste bag, and a spool valve positioned in line with the effluent waste tube.