The morphological, electric, and dielectric properties of water-based conjugated polymer blends, such as polypyrrole:polystyrene sulfonate (PPy:PSS) or poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS), are known to be influenced by the water content. These properties also influence the macroscopic performance when the conjugated polymer blends are employed in a device. An in situ humidity-dependence study on thin films of PPy:PSS by Kelvin probe force microscopy (KPFM) is presented. A particular KPFM mode, dielectric imaging, is used, which detects the second harmonic electrostatic force. Thin PPy:PSS films are drop-coated on hydrophobic graphite substrates. Upon increasing the relative humidity, the hydrophilic PSS is swelled and dewetted on the substrate, while the hydrophobic PPy remains almost unchanged. The swelling and dewetting of PSS results in irreversible morphological changes in the thin films, as well as nanoscopic rearrangement on the surface of the PPy:PSS films. The nanoscopic rearrangement can only be detected by dielectric imaging. It is also observed that relative humidity affects unannealed and thermally annealed PPy:PSS thin films differently.