<p>Evaluating recharge characteristics is crucial for groundwater resource management. However, assessing groundwater recharge characteristics under high-frequency water table fluctuations still requires further research. This study presented a comprehensive application of a denoising method, time series techniques, and the water table fluctuation method for solving the problem of high-frequency water table in groundwater recharge studies. Results of correlation and cross-wavelet analysis showed that, for the study area, the lag time between water table and recharge was in the range of 56–176 days, and its spatial distribution had a significant positive correlation with water table depth. In addition, it was revealed that the recharge-induced water table rise showed temporal variation, featuring a gradually decreasing rate of water table rise from January to May, an increasing rate from June to August, and a relatively stable rise from September to December. Moreover, the groundwater recharge in 2020 ranged from 78.8 to 380.8 mm (with an average of 191.5 mm). Groundwater recharge showed a significant rise in 2021 and 2022, resulting from extreme rainfall in 2021 and ecological water replenishment in 2021 and 2022. Furthermore, the spatial distribution of annual recharge and cross-wavelet analysis results revealed that the ecological water replenishment had taken an important recharge role in the area along the Yongding river northwest of Guangyang region. The comprehensive integration of multiple methods for identifying recharge characteristics under conditions with high-frequency water table fluctuations can provide a reference for other studies, and findings can support an understanding of the local groundwater recharge.</p>