Unusual decreases of water levels were consistently observed in 78% (Combining double low line 42/54) of wells in the Choshuichi Alluvial Fan of central Taiwan about 250 days before the Chi-Chi earthquake (M Combining double low line 7.6 on 20 September 1999) while possible factors of barometric pressure, earth tides, precipitation as well as artificial pumping were removed. Variations in groundwater levels measured on anomalous wells from 1 August 1997 to 19 September 1999, which covers the 250 day unusual decreases, were transferred into the frequency domain to unveil frequency characteristics associated with the Chi-Chi earthquake. Analytical results show that amplitudes at the frequency band between 0.02 day-1 and 0.04 day-1 generally maintained at the low stage and were apparently enhanced a few weeks before the Chi-Chi earthquake. Variations of amplitude at this particular frequency band were further examined along with other Taiwan earthquakes (M> 6) from 1 August 1997 to 31 December 2009. Features of the enhanced amplitudes at the frequency band are consistently observed prior to the other two earthquakes (the Rei-Li and Ming-Jian earthquakes) during the 12.5 yr study period. In addition, surface displacements recorded from GPS, which provides insights into understanding stress status in subsurface during the Chi-Chi earthquake, are also inspected. The result confirms that abnormal rise and fall changes in groundwater level yield an agreement with forward and backward surface displacements around the epicentre prior to the Chi-Chi earthquake.