The performance stability of organic photovoltaics (OPVs) is largely determined by their nanoscale morphology and composition and is highly dependent on the interaction with oxygen and water from air. Low-dose cryo-(S)TEM techniques, in combination with OPV donor-acceptor model systems, can be used to assess oxygen- and water-uptake in the donor, acceptor and their interface. By determining a materials dependent critical electron dose from the decay of the oxygen K-edge intensity in Electron Energy Loss Spectra, we reliably measured oxygen- and water-uptake minimizing and correcting electron beam effects. With measurements below the dose limit the capability of STEM-EDX, EFTEM and STEM-EELS techniques are compared to qualitatively and quantitatively measure oxygen and water uptake in these OPV model systems. Here we demonstrate that oxygen and water is mainly taken up in acceptor-rich regions, and that specific oxygen uptake at the donor-acceptor interphase does not occur. STEM-EELS is shown to be the best suitable technique, enabling quantification of the local oxygen concentration in OPV model systems.