New methods and apparatus are described for assessing the integrity of a separation module or filtration system. A principle embodiment concerns use of a transient pulse of challenge species to probe a spiral wound module. The resulting time-dependent concentration of challenge species in the permeate is detected, recorded, and compared to a reference. An apparatus is further claimed for detecting permeate conductivity at multiple points within the permeate collection tube of a spiral wound module. Also disclosed is a process whereby the permeate stream from a filtration system is concentration by a high recovery membrane apparatus prior to measurement of challenge species concentration.