The device is suitable in particular for treating medical endoscopes. At least one treatment fluid is fed through a conduit system (3) to a channel attachment (4), to which a channel of the instrument to be treated can be attached. The conduit system has a fluid attachment (39), which can be connected to a source of treatment fluid. With the aid of a measuring device, the flow of the treatment fluid in the conduit system, and thus the permeability of the attached channel, can be measured. The measurement is effected with the aid of a measurement section (6) in which a flow sensor (7, 7′) is arranged. All the treatment steps are carried out via the conduit system and in particular also via the measurement section. In this way, the conduit system is subjected to the same process as the instrument to be treated, and a flow measurement can be carried out in each individual treatment step.