Natural soil systems usually exhibit complex properties such as fractal geometry, resulting in complex dynamics for the movement of pollutants. This study developed a fractional advection-dispersion-reaction equation (fADRE) to quantify nitrate transport in soil systems. Applications showed that the fADRE model can quantify both hydrological and biogeochemical impacts on the fate and transport of nitrate in various saturated soils. The qualitative relationship between model parameters and the target system properties was also explored in detail.