Conducting polymers are an interesting class of materials that can be tuned to have a range of properties through counterion doping. For most conducting polymers, the insertion of anions (the doping process) leads to the formation of carbocations (positive charge carriers) along the conjugated polymer backbone. In this research, we report on a scenario that arises where certain (commonly used) anions in water induce oxygenation of the conducting polymers heteroatom. This is in contrast to the widely reported doping process, and the recently reported hydrolysis of conducting polymers. We observe that the transition between these different conducting polymer-interactions/reactions is well described by the concept of structure-making and structure-breaking anions. Poly(3,4-propylenedioxy thiophene dimethyl) (PProDOT-Me 2 ), polypyrrole (PPy), and poly(3,4-ethylenedioxy thiophene) (PEDOT) thin films are exposed to a range of anions in water. Both PProDOT-Me 2 and PPy are susceptible to oxygenation, while in contrast PEDOT is doped, when exposed to structure-breaking anions. All the polymers show hydrolysis for structuremaking anions. The knowledge of the interaction and/or reaction of conducting polymers with anions in water is not only critical to their application in devices for aqueous environments (i.e., sensing), but also for their processing and fabrication using water.