The double-holding water tank system is a common non-linear control system that plays a crucial role in process control in the chemical industry. It consists of two cylindrical glass containers: the preset tank and the main tank. The main challenge in controlling this system is adjusting the main control valve to ensure that the actual liquid level of the main tank tracks the desired liquid level. This paper explores the zeroing dynamics (ZD) method and its application in tracking control. A non-linear model is developed for the double-holding water tank system, and the ZD method is used to design an effective controller (called the ZD controller) for tracking control. Additionally, the robustness of the double-holding water tank system in the presence of time-varying perturbations is investigated. In order to substantiate the effectiveness and robustness of the ZD controller, simulation experiments on four different tracking trajectories corresponding to four different practical situations, as well as an extra simulation experiment considering time-varying perturbations, are conducted. Furthermore, a comparative simulation experiment based on the backstepping method is conducted. The presented results successfully illustrate the feasibility and effectiveness of the ZD method for the tracking control of double-holding water tank systems.