A comparison of detection limits of gas chromatography-mass spectrometry (GC-MS) in selected ion monitoring (SIM) with gas chromatography-tandem mass spectrometry (GC-MS/MS) in selected reaction monitoring (SRM) mode with both electron ionization (EI) and negative-ion chemical ionization (NCI) are presented for over 50 pesticides ranging from organochlorines (OCs), organophosphorus pesticides (OPs) and pre-emergent herbicides used in the Canadian prairies (triallate, trifluralin, ethalfluralin). The developed GC-EI/SIM, GC-NCI/SIM, and GC-NCI/SRM are suitable for the determination of pesticides in air sample extracts at concentrations <100 pg µL−1 (<100 pg m−3 in air). No one method could be used to analyze the range of pre-emergent herbicides, OPs, and OCs investigated. In general GC-NCI/SIM provided the lowest method detection limits (MDLs commonly 2.5–10 pg µL−1) along with best confirmation (<25% RSD of ion ratio), while GC-NCI/SRM is recommended for use where added selectivity or confirmation is required (such as parathion-ethyl, tokuthion, carbofenothion). GC-EI/SRM at concentration <100 pg µL−1 was not suitable for most pesticides. GC-EI/SIM was more prone to interference issues than NCI methods, but gave good sensitivity (MDLs 1–10 pg µL−1) for pesticides with poor NCI response (OPs: sulfotep, phorate, aspon, ethion, and OCs: alachlor, aldrin, perthane, and DDE, DDD, DDT).