Aqueous solutions of the conjugated polymer poly(2,5-disulfopropoxy-1,4-phenylene vinylene) (DPS-PPV) blended with poly(vinyl alcohol) (PVA) have been exposed to Couette shear flow and studied using fluorescence techniques. Significant aggregation of the DPS-PPV and PVA molecules occurred during shear exposure, resulting in an 80% decrease in solution fluorescence intensity and formation of visible polymer particles. The aggregation process caused a separation of the DPS-PPV molecules where the fluorescence of the aggregated particles had a red-shifted emission peak at a wavelength of 594 nm, and the remaining solution had a blue-shifted emission at 513 nm, as compared to an initial emission peak at 574 nm. The fluorescence excitation spectra of the aggregated particles became broadened while the excitation peak of the remaining solution narrowed. This has great implications for the processing of aqueous conjugated polymer systems in various polymer blends, because aggregation could cause significant problems for device manufacture.