Hierarchically oriented plasmonic nanostructures have attracted an advanced molecular sensing platform for multifaceted applications. In the present work, we have attempted to fabricate ultrasensitive and cost-effective pyramidal/nanowire hetero arrays, hosted with silver nanoparticles for the effective surface-enhanced Raman spectroscopy (SERS) assisted detection of toxic water contaminants. Three-dimensionally oriented pyramidal/nanowire hetero arrays with enhanced surface area were fabricated by combining wet etching and metal-assisted chemical etching techniques. The regulation of structural features was achieved by controlling the process parameters during fabrication. Particularly, the evolution of morphological properties of the hybrid sensor was investigated in terms of nanowire aspect ratio and further analyzed in terms of SERS properties. The hetero arrays exhibited significant enhancement in Raman signal for sensing organic pollutants. Moreover, these hetero arrays with a nanowire length of ∼1 µm exhibited the highest signal enhancement. Further, the excellent reproducibility and reusability characteristics were also demonstrated for the fabricated sensors. Different cationic and anionic organic pollutants were employed for efficacy studies which showed detection limits ranging from femtomolar to picomolar levels. Finally, the real-time sensing of organic contaminants such as aniline was also investigated from seawater with an estimated enhancement factor of 8 × 108, indicating that as-fabricated hetero arrays can perform as outstanding SERS sensors for environmental remediation applications.