The transfer of pesticides from agricultural soils to food and drinking water is a major health issue. There are actually few robust methods to identify, characterize and quantify the dissipation of pesticides in complex media such as soils, waters and sediments. Here, we review multi-elemental compound-specific isotope analysis to study sources and transformations of pesticides in agricultural soils. First, we discuss advanced extraction and purification techniques for pesticides in soils. Then, analytical techniques for reliable measurements of the stable isotope composition of the pesticides are presented. We report a unique dataset of 547 isotopic compositions of 71 active molecules produced by various pesticide manufacturers, for the following isotopes: 13C, 15N, 37Cl, and 2H. We also report 270 isotope fractionation values for 33 compounds, which might help to elucidate the mechanisms of pesticide transformation by biodegradation, photodegradation and other abiotic processes. Compounds include legacy pesticides such as atrazine, lindane, dichlorodiphenyltrichloroethane, chlordecone and organophosphorus compounds. Transformation processes may be identified and quantified using the Rayleigh concept for isotope fractionation during reaction.