A water-soluble polythiophene with pendant phosphonic acid groups, poly(3-(3'-thienyloxy)propane-phosphonate) (P3TOPP), has been synthesized. Matrix-assisted laser desorption ionization (MALDI) measurements showed that P3TOPP is an oligomer with an average chain length of 10 monomer units. In aqueous solutions it could be electrochemically oxidized and displayed self-acid doping at pH below 13. P3TOPP was used to prepare polyelectrolyte multilayers with poly(diallyldimethylammonium chloride) (PDADMA) and metal phosphonate multilayers with Zr4+ ions by the sequential layer-by-layer technique. The films were characterized by electrochemistry, atomic force microscopy (AFM), UV-vis, IR, and X-ray photoelectron (XPS) spectroscopy. A regular layer-by-layer growth was observed with both types of multilayers. The nature of the films was probed with XPS, which showed that the observed binding energies were characteristic for metal phosphonates and polyelectrolyte multilayers in Zr/P3TOPP and P3T0PP/PDADMA films, respectively. In the former, the Zr:P ratio showed deviation from the theoretical stoichiometry, and the reasons for the nonstoichiometry are discussed. In the latter, the N:P ratio was consistent with the partial deprotonation of the phosphonate groups. The multilayers exhibited both electrochromism and pH-induced halochromism.