Oxygen vacancies in tungsten trioxide (WO₃) nanostructures (WO_3−x) dominate the major characteristics of the material and determine their activity in various applications including photocatalysis and surface-enhanced Raman spectroscopy (SERS). Despite some studies performed in the last decade, the photocatalytic activity toward different pollutants and SERS activity toward different Raman reporter molecules are still unclear and may provide valuable insights into this research field. Therefore, in this study, we propose WO_3−x nanowires (NWs) both as ideal photocatalysts for the degradation of organic pollutants such as crystal violet (CV), methylene blue (MB), malachite green (MG), and rhodamine 6G (R6G) and a SERS platform for the detection of these molecules. In the first step, WO_3−x NWs were fabricated through the solvothermal method. Afterward, the oxygen vacancy content of WO_3−x NWs was manipulated by the addition of silver ions or H₂O₂. Although H₂O₂ led to a remarkable decrease in oxygen vacancies (WO₃), the addition of silver ions led to the formation of Ag nanostructures on WO_3−x NWs (WO_3−x@Ag). Interestingly, the combination of WO_3−x and WO_3−x@Ag nanosystems with all dye molecules resulted in the formation of H-aggregates due to the strong electrostatic interaction between the nanostructure and dye molecules and then its photocatalytic degradation, while regular degradation of dyes was observed for WO₃. In SERS activity tests, each NP system exhibited different activities depending on various parameters including the chemical nature of the nanosystem, the degree of oxygen vacancy, the interaction of the Raman reporter molecule with the surface of the NP, and the resultant formation of H-aggregates or photocatalytic degradation. The combination of MB with WO_3−x, WO_3−x@Ag, and WO₃ created enhancement factors such as 1.6 × 10³, 5.4 × 10³, and 6.2 × 10³, respectively. This report showed that the parameters mentioned here must be considered in detail to evaluate the photocatalytic and SERS activity of the WO₃-based nanosystem.