Isoproturon is a selective herbicide belonging to the phenylurea family and widely used for pre- and post-emergence control of annual weeds. Soil amendments (e.g. organic compounds or dissolved organic matter) may affect environmental behavior and bioavailability of pesticides. However, whether the physiochemical process of isoproturon in soils is affected by organic amendments and how it is affected in different soil types are unknown. To evaluate the impact of low molecular weight organic acids (LMWOA) and dissolved organic matter (DOM) on sorption/desorption and mobility of isoproturon in soils, comprehensive analyses were performed using two distinct soil types (Eutric gleysols and Hap udic cambisols). Our analysis revealed that adsorption of isoproturon in Eutric gleysols was depressed, and desorption and mobility of isoproturon were promoted in the presence of DOM and LMWOA. However, the opposite result was observed with Hap udic cambisols, suggesting that the soil type affected predominantly the physiochemical process. We also characterized differential components of the soils using three-dimensional excitation–emission matrix (EEM) fluorescence spectroscopy and Fourier transform infrared (FT-IR) spectroscopy and show that the two soils displayed different intensity of absorption bands for several functional groups.