Structural composition of soil organic matter and the adsorption/desorption characteristics of the insecticide chlorpyrifos were investigated in two soil profiles (Andisol and Entisol) under agriculture production using Fourier transform infrared spectroscopy, nuclear magnetic resonance, and batch analysis methods. Throughout the soil profile, the Andisol had larger values of pH, organic carbon content, cation exchange capacity (CEC), and effective CEC than the Entisol. The Entisol showed larger amounts of kaolinite and ferric and/or aluminum oxides in deeper soil layers. Soil organic matter carbonyl-C, aryl-C, O-alkyl C, and alkyl-C were transported vertically in the vadose zone, with aryl-C being the predominant species in both soils. These results suggest that aryl-C is a reasonable predictor of chlorpyrifos adsorption properties under tropical conditions. Chlorpyrifos adsorption was found to be spontaneous and exothermic, with decreasing adsorption values of the distribution coefficient Kd (37.2–10.1 L kg−1) in the deeper layers of both soil types (although more significant in the Entisol). One-step desorption hysteresis showed a monotonic decrease with increasing soil depth and correlated positively with both organic carbon and CEC. The degradation of chlorpyrifos in Andisol (0–100 cm) was investigated using a laboratory incubation method. Degradation rate k was found to be approximately constant (0.011–0.015 d−1) throughout the soil profile where biotic and abiotic processes are active. Based on the Groundwater Ubiquity Score, chlorpyrifos presented a “transitional” leaching potential with soil depth.