The spatial distribution of reaction products in multilayer polymer solar cells induced by water and oxygen atmospheres was mapped and used to elucidate the degradation patterns and failure mechanisms in an inverted polymer solar cell. The active material comprised a bulk heterojunction formed by poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) sandwiched between a layer of zinc oxide and a layer of poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS) that acted as, respectively, electron and hole transporting layers between the active material and the two electrodes indium-tin-oxide (ITO) and printed silver. X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) in conjunction with isotopic labeling using (H2O)-O-18 and O-18(2) enabled detailed information on where and to what extent uptake took place. A comparison was made between the use of a humid (oxygen-free) atmosphere and a dry oxygen atmosphere during testing of devices that were kept in the dark and devices that were subjected to illumination under simulated sunlight. It was found that the reactions taking place at the interface between the active layer and the PEDOT:PSS were the major cause of device failure in the case of these inverted devices, which are compatible with full roll-to-roll (R2R) coating and industrial manufacture. The PEDOT:PSS was found to phase separate, with the PEDOT-rich phase being responsible for most of the interface degradation in oxygen atmospheres. In water atmospheres, little chemically induced degradation was observed, whereas a large partially reversible dependence of the open circuit voltage on the relative humidity was observed. In addition, temporal aspects are discussed in regard to degradation mechanisms. Finally, analytical aspects in regard to storing devices are discussed.