A magnetic resonance detection (MRD) system for and methods of detecting and classifying multiple chemical substances is disclosed. In one example, the presently disclosed MRD system is a nuclear quadrupole resonance (NQR) detection system that provides multi-frequency operation for substantially full coverage of the explosive NQR spectrum using a broadband transmit/receive (T/R) switch (or duplexer) and a single multi-frequency radio frequency (RF) transducer. More particularly, the MRD system provides a frequency-agile system that can operate over a wide band of frequencies or wavelengths. Further, a method of detecting and classifying various chemical substances is provided that includes pulse sequencing with “frequency hopping,” phase cycling for reducing or substantially eliminating background noise, and/or a process of mitigating amplitude modulation (AM) radio interference.