When a solute transport process is viewed as a dynamic system with input and output, a system identification technique can be used to study it from input-output data. According to the design of excitation signals in the system identification approach, the commonly used rectangular pulse as input signal for column experiments is not optimum because it does not simultaneously meet the requirements for exciting the studied transport process, i.e., possessing frequency components with high enough amplitude and wide enough passband. In this article, stepped sine signals were proposed to replace the rectangular pulse because their amplitude and passband can be independently chosen. The stepped sine signals of concentration were generated by a High Performance Liquid Chromatography (HPLC) and used as the input for the column experiments to identify parameters of the convection-dispersion equation (CDE) and mobile-immobile model (MIM). In order to test the effect of noise on the identification of transport process, numerical experiments were carried out to identify the CDE under white noise when the input was designed as stepped sine functions and rectangular pulse. The results of the numerical experiments showed that the input signal of a sine function was more robust and accurate in process identification than that of a rectangular pulse.