I agree with first answer, but the rate of flow through it may be difficult to measure. Who is to say that the aquitard is of uniform thickness or density, solid or fractured? I don't know how you might do it, and hopefully you have an approach, but I added a paper (Garrett...) that used water quality differences to try to separate out rain derived surface waters from shallow and deeper groundwaters.
In measuring flow indirectly by applying a water balance approach (ie, water table changes), I would consider that groundwater flow may have three dimensional considerations, if it cannot be processed vertically downward with gravity through the aquitard, it may move laterally away from the confining material. If within rooting zone, transpiration stress on water table confined by aquitard suggests some water stored or detained by the aquitard might be pulled upward. Actively growing pine trees may transpire nearly a meter of water in a year. It sounds like an interesting subject, I can imagine that the variability in aquitards could be substantial, so I probably have more questions than you do.
I agree with the aforementioned answers. Also, you can take a look at the book titled "Multilayerd aquifer systems" (Alexander H.D Cheng, 2000) chapter 6: multilayerd aquifer theory.