With a liquid chromatographic column, the transport behaviors of malathion and Cl− in red soil and gray fluvo-aquic soil columns were studied. Malathion was leached with three different solutions (0.01 mol L−1 CaCl2, 0.01 mol L−1 CaCl2 + 0.001 mol L−1 citric acid, and 0.01 mol L−1 CaCl2 + 0.001 mol L−1 malic acid) at two pore water velocities (0.191 and 0.382 cm min−1). The symmetrical breakthrough curves (BTCs) of Cl−, which were obtained by using the conservative tracer, showed no significant physical nonequilibrium in solution transport. Compared with those of Cl−, the BTCs of malathion were obviously asymmetrical, with a shift to the right and an extended long-time tail, which is typical of sorption nonequilibrium. Using CXTFIT2.1 and continuous time random walk (CTRW) theory, the physical and hydrodynamic parameters were obtained by fitting the experimental results to the measured BTCs. For both the local equilibrium assumption (LEA) model and the nonequilibrium two-site model (TSM), introduction of a decay term improved the fitting of BTCs, which indicated that sorption–desorption influenced malathion transport. On the whole, the TSM fitted the BTCs better than the LEA model because the TSM accounted for either sorption- or transport-related nonequilibrium. Under most experimental conditions, compared with the LEA and TSM, the CTRW described the distal portion, especially the extended long-time tails, of BTCs better because non-Fickian diffusion arose at later transport times. The results suggest that the nonequilibrium TSM is a useful approach to predict malathion transport. At later transport times, however, the CTRW, characterizing non-Fickian transport, better explained the BTC tails. These results are valuable to predict and control the fate of malathion in the environment.