Transitions in the backbone conformation of polythiophenes (PTs) in organic solvents, measurable spectroscopically, have been widely observed to influence thin-film morphology; however, such conformational transitions of water-soluble PT derivatives, with respect to their intramolecular versus intermolecular origin, remain largely obscure. Here, we report on dynamic conformational transitions of poly(3-potassium hexanoate thiophene) in aqueous cetyltrimethylammonium bromide investigated by means of Fourier transform infrared spectroscopy, differential scanning calorimetry, polarizing optical microscopy, and ultraviolet-visible absorption and fluorescence spectroscopy. As-prepared complexes exist as stable hydrogels. Upon dilution, a significant time-dependent chromism occurs spontaneously. A coil-to-rod conformational transition is identified in this mechanism. Study into the corresponding kinetics demonstrates an inverse first-order rate law. It is found that the conformational transition is thermally reversible and concentration-independent. The critical transition temperature is largely dependent on the surfactant architecture. A theoretical model is presented to explain this new phenomenon and the mechanisms behind its influence on the optoelectronic properties.