Perchlorate (ClO4−) contamination has received increased attention the past two decades because of health concerns from its impact on thyroid function coupled with its environmental ubiquity and persistence. Here we demonstrate the detection of ClO4− below micromolar (<1 × 10−6 moles l−1) levels using a portable Raman instrument integrated with novel elevated gold (Au) ellipse dimer nanoantenna surface enhanced Raman scattering (SERS) architectures. The ellipse dimer nanoantenna architectures demonstrate improved ClO4− detection limits over previously reported SERS substrates while maintaining good reproducibility. The impact of chloride (Cl−), nitrate (NO3−), and sulfate (SO42−) interferences on the detection efficiency is systematically evaluated; SO42− is found to exhibit the largest interference effect at low concentrations while at higher ion concentrations the interference effects among ions are similar. Additionally, ClO4− concentrations on the order of 1 mg l−1 are determined in groundwaters collected from an US Department of Defense Navy site demonstrating the applicability of these SERS architectures for the rapid, field detection of trace‐level ClO4− contamination within complex environmental samples. Copyright © 2016 John Wiley & Sons, Ltd.