The use of surface enhanced Raman spectroscopy in the development of low cost, portable sensor devices that can be used in the field for nitroguanidine neonicotinoid insecticide detection is appealing. However, a key challenge to achieving this goal is the lack of detailed analysis and vibrational assignment for the most popular neonicotinoids. To make progress toward this goal, this paper presents an analysis of the bulk Raman and SERS spectra of two neonicotinoids, namely clothianidin and imidacloprid. Combined with first-principles simulations, this allowed assignment of all Raman spectral modes for both molecules. To our knowledge, this is the first report of SERS analysis and vibrational assignment of clothianidin, and a comprehensive assignment and analysis is provided for imidacloprid. Silver nanostructured surfaces were fabricated for qualitative SERS analysis, which provides the characteristic spectra of the target molecules and demonstrates the ability of SERS to sense these molecules at concentrations of 1 ng/mL. These concentrations are on par with high-end chromatographic-mass spectroscopy laboratory methods. These SERS sensors thus allow for the selective and sensitive detection of neonicotinoids and provide complementary qualitative data for the molecules. Furthermore, this technique can be adapted to portable devices for remote sensing applications. Further work focuses on integrating our device with an electronics platform for truly portable residue detection.