This study applies a novel concept to decompose water stages to understand the factors that affect an estuary. The estuary water stages vary due to different complex, often nonlinear and non-stationary factors. Therefore, it is very difficult for researchers to break down water stages into contributing factors with single integrated methods. The Hilbert Huang transform (HHT) is an easy to use, efficient and powerful method of processing non-stationary, non-linear signals to optimize a complicated data process. The HHT is composed of empirical mode decomposition (EMD) and Hilbert transform. EMD decomposes the water stages into several intrinsic mode functions (IMFs). Through the Hilbert transform, IMFs could obtain amplitude and instantaneous frequency with time. Those IMFs with amplitude and frequency can be used to represent those factors that affect the water stages in an estuary. However, the physical meanings represented by IMFs should be inferred in conjunction with the other hydrological data. This study uses Tanshui River estuary water stages to show HHT applied to determining the factors that affect the water stages. HHT application provides a methodology for others to follow to identify the water stage components in an estuary.