The study applies a novel concept to decompose a water stage for understanding the affecting factors in an estuary. Water stages in an estuary vary on different factors, which are complex and often nonlinear and non-stationary. Therefore it is very difficult for the researchers to break down water stages into affecting factors with single integrated methods. The Hilbert Huang transform (HHT) is an easy to use, efficient and powerful method of processing non-stationary and non-linear signals to optimize the process of complicated data from water stages in an estuary. The HHT composed of empirical mode decomposition (EMD) and Hilbert transform. EMD decompose the water stages into several intrinsic mode functions (IMFs). Through Hilbert transform, IMFs could get amplitude and instantaneous frequency with time. Those IMFs with amplitude and frequency can be used to represent factors affecting 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 the water stages of the Tanshui River estuary to show the application of HHT for determining factors affecting the water stages. Through the application of HHT, it can provide the methodology for others to follow for identifying the components of water stages in an estuary.