This study demonstrates the fabrication of mesoporous tungsten trioxide (WO₃)-decorated flexible polyimide (PI) electrodes for the highly sensitive detection of catechol (CC) and hydroquinone (HQ), two environmental pollutants. Organic–inorganic composite dots are formed on flexible PI electrodes using evaporation-induced self-assembly (EISA) and electrospray methods. The EISA process is induced by a temperature gradient during electrospray, and the heated substrate partially decomposes the organic parts etched by O₂ plasma, creating mesoporous structures. Differential pulse voltammetry and cyclic voltammetry demonstrate a linear correlation between analyte concentration and the electrochemical response. Computational studies support the spontaneous adsorption of CC and HQ molecules on model WO₃ surfaces. The proposed sensor shows high sensitivity, a wide linear range, and a low detection limit for both individual and simultaneous determination of CC and HQ. Real sample analysis on river water confirms practical applicability. The WO₃-decorated PI electrode presents an efficient and reliable approach for detecting these pollutants, contributing to environmental safety measures.