The newly developed Fractional Advection-Dispersion Equation (FADE), which is FADE was extended and used in this paper for modelling adsorbing contaminant transport by adding an adsorbing term. A parameter estimation method and its corresponding FORTRAN based program named FADEMain were developed on the basis of Nonlinear Least Square Algorithm and the analytical solution for one-dimensional FADE under the conditions of step input and steady state flow. Data sets of adsorbing contaminants Cd and NH4+-N transport in short homogeneous soil columns and conservative solute NaCI transport in a long homogeneous soil column, respectively were used to estimate the transport parameters both by FADEMain and the advection-dispersion equation (ADE) based program CXTFIT2.1. Results indicated that the concentration simulated by FADE agreed well with the measured data. Compared to the ADE model, FADE can provide better simulation for the concentration in the initial lower concentration part and the late higher concentration part of the breakthrough curves for both adsorbing contaminants. The dispersion coefficients for ADE were from 0.13 to 7.06 cm2/min, while the dispersion coefficients for FADE ranged from 0.119 to 3.05 cm1.856/min for NaCI transport in the long homogeneous soil column. We found that the dispersion coefficient of FADE increased with the transport distance, and the relationship between them can be quantified with an exponential function. Less scale-dependent was also found for the dispersion coefficient of FADE with respect to ADE.