We have fabricated 3D surface enhanced Raman scattering (SERS) substrates composed of silver-coated gold nanorods (Ag/AuNRs) supported on polycaprolactone (PCL) electrospun fibers for use as sensors of environmental contaminants. The successful fabrication and immobilization of Ag/AuNRs onto PCL fibers further demonstrates the universal nature of our fabrication strategy, benefiting from immobilization based on electrostatic attraction, a nonspecific interaction. For the first time, Ag/AuNRs with different Ag coating thicknesses have been synthesized, characterized by UV-vis spectroscopy and electron microscopy, and assembled onto PCL fibers. The variation of the Ag coating thickness allows the tuning of the surface plasmon resonance (SPR) so as to be in close proximity to the laser wavelength of the probing laser. Using 4-mercaptopyridine (4-Mpy) as a probe molecule, the SERS performance of the Ag/AuNR-based SERS substrate has been investigated. This substrate allowed detection of 4-Mpy at a concentration as low as 10 nM with excellent reproducibility. SERS substrates fabricated with Ag/AuNRs with different Ag coating thicknesses have been compared with substrates using AuNRs. It was found that when fabricated with a Ag coating, the substrates exhibited larger SERS enhancement than that found for substrates fabricated with AuNRs alone. This could be attributed to electron transfer between the gold core and silver shell in a bimetallic rod-shaped nanostructure. In addition, considering the surface chemistry provided by silver coating, we have demonstrated that this new SERS substrate can be used as an environmental sensor for arsenic detection.