Advances in nanofabrication have allowed the production of new and more reproducible substrates for the Raman detection of trace antimicrobials in water. The superior substrate uniformity combined with the ability to control surface morphology represents a significant step forward in the design of substrates with improved enhancement factors and trace-detection capabilities. The work presented herein successfully combines electron-beam lithography (EBL) and reactive ion-etching (RIE) protocols for the construction, testing, and validation of plasmonic hybrid morphology nanoarrays for the detection of arsenic antimicrobials in water. The fabricated substrates consist of 2500 μm(2) Ag-coated silicon dioxide (SiO2)/Si pillar nanoarrays of alternating hexagonal and elliptical features. Control of simple fabrication parameters such as inter-particle spacing (gap) and its orientation relative to the laser polarization vector (parallel or orthogonal) result in over a tenfold improvement in the apparent Raman response under optimized conditions. At a 633 nm excitation frequency, the best substrate performance was observed on parallel-oriented features with a 200 nm gap, with over one order of magnitude increase in the apparent surface-enhanced Raman scattering (SERS) signal relative to standard silver-polydimethylsiloxane (Ag-PDMS) nanocomposites. Monitoring of the characteristic As-C stretching band at 594 cm(-1) allowed the detection of arsenic antimicrobials in water well within the parts per million range. Calculated surface-enhancement factors (SEF) for this substrate, employing 532, 785, and 633 nm excitation wavelengths, was within five, six, and seven orders of magnitude, respectively. The effect of substrate morphology and nanofabrication process on the Raman enhancement factor is presented.