Groundwater level in wells, i.e., well water level (WWL) is an important index in hydrological monitoring during earthquakes. Due to the complex dynamics of groundwater, the WWL might change under seismic actions. This paper attempts to identify the long-term correlation between WWL and earthquakes, and disclose the topological features of groundwater dynamics. Taking Nanxi Well as an example, the authors conducted state space analysis on the raw series and trend of WWL to eliminate interferences like barometric pressure, rainfall, and solid tide, creating the trend time series. Then, the raw series and trend time series were converted into the raw visible graph (VG) network and trend VG network, respectively. Further, the global period was divided into five local time windows, and the two VG networks were compared by global aspect, local aspect, and topological properties of complex networks. The results show that the nodes of high degrees are closely related to the seismic response of the WWL in Nanxi Well; all VG networks are scale free and hierarchical; the seismic response of the WWL in the well is reflected by degree correlation; the community division of raw VG network was basically the same as that of trend VG network. The research findings provide insights to the seismic response of WWL and the dynamic fluctuation of groundwater level.