Tungsten oxide nanostructures were modified by oxygen vacancies through hydrothermal treatment. Both the crystalline structure and morphological appearance were completely changed. Spherical WO3·H2O was prepared from tungstic acid solution by aging at room temperature, while rod-like WO3·0.33H2O was prepared by hydrothermal treatment of tungstic acid solution at 120 °C. These structures embedded in sodium alginate (SA)/polyvinylpyrrolidone (PVP) were synthesized as novel porous beads by gelation method into calcium chloride solution. The performance of the prepared materials as photocatalysts is examined for methylene blue (MB) degradation in aqueous solutions. Different operation parameters affecting the dye degradation process, such as light intensity, illumination time, and photocatalyst dosage are investigated. Results revealed that the photocatalytic activity of novel nanocomposite changed with the change in WO3 morphology. Namely, the beads with rod nanostructure of WO3 have shown better effectiveness in MB removal than the beads containing WO3 in spherical form. The maximum degradation efficiency was found to be 98% for WO3 nanorods structure embedded beads, while the maximum removal of WO3 nanospheres structure embedded beads was 91%. The cycling-ability and reuse results recommend both prepared structures to be used as effective tools for treating MB dye-contaminated wastewaters. The results show that the novel SA/PVP/WO3 nanocomposite beads are eco-friendly nanocomposite materials that can be applied as photocatalysts for the degradation of cationic dyes in contaminated water.