Abstract: The karst groundwater level in the main urban area of Nanjing is influenced by both precipitation recharge and human extraction activities, making it one of the key factors inducing Karst collapse disasters and posing a serious threat to urban geological safety. To investigate the dynamic relationship between Karst groundwater levels and precipitation, this study adopted observed precipitation data and Karst groundwater monitoring records from 1989 to 2020 in Nanjing’s main urban area. By integrating the CUSUM mutation detection technique, continuous wavelet transform, and wavelet coherence analysis, the study systematically analyzed variations and correlations between precipitation and groundwater levels. The results indicate that before May 2008, groundwater levels in the exposed Karst areas were jointly affected by precipitation recharge and human extraction. After May 2008, however, groundwater variations in these areas were predominantly controlled by precipitation. In the covered Karst areas, a turning point appeared in May 2000: prior to this, groundwater level fluctuations were jointly influenced by extraction and precipitation, whereas afterward they became primarily governed by precipitation. Further analysis revealed significant resonance periods between groundwater levels and precipitation at 0.5-year, 1-year, and 2-year time scales in the exposed Karst areas. In contrast, in the covered Karst areas, clear resonance patterns were observed at 0.5-year, 1-year, 2-year, and 6-year scales. Notably, the correlation between groundwater levels and precipitation was significantly closer in the covered Karst areas than that in the exposed, suggesting that groundwater in covered Karst settings responds more sensitively to precipitation variability. This study provides a scientific basis for the prediction and early warning of Karst groundwater level fluctuations and offers valuable technical support for the prevention and control of urban Karst collapse disasters.