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Understanding of behavior, variability, and links between hydrological series is a key element for successful long-term water resources planning and management. In this study, various time-scale-based methods such as correlation and spectral analysis (CSA), cross wavelet (XWT), and wavelet coherence transform (WCT) were applied to assess the response of daily rainfall and karst spring discharge for the Sebaou River basin, which is located on Mediterranean basin in northern Algeria. The CSA revealed that the hydrogeological systems under study are characterized by various memory effect (small, poor, reduced, and extensive) with regularization times ranging from 5 to 50 day. XWT between rainfall and discharge time series indicates few marked disruptions in the spectra between the 1980s and 1990s corresponding to the dry period. The annual process is visible, dominant, and more amplified compared to the multi-annual fluctuations that characterize the 1-3- and 3–6-year modes, which explained the multi-annual regulation. The nonlinear relationship of the short-term components seems to be linked to the periods of storage (infiltration). Compared to the WCT components of 2–5, 26, and 52 weeks, there is a strong coherence for 102 weeks, which explains the long-term component, indicating a quasi-linearity of the rainfall-runoff relationship. According to the obtained results, the construction of more water resources structures is recommended to increase the water storage and improve the water supply due to the richness of the hydrographic network. On the other hand, the impacts of human activities on streamflow due to the looting of rocks and sands in the Sebaou River valleys have reached alarmingly high levels that require urgent intervention for the protection of water and ecological resources and their better rational use.