•Advanced application of time series analysis in complex karst systems.•Wide spatial distribution of monitoring points and high temporal data resolution.•Cross-correlation analysis not sufficient to study the effects of allogenic recharge.•An innovative approach using partial cross-correlation analysis (PCCF) is presented.•PCCF enables separation of the effects of allogenic and autogenic recharge. Karst aquifers have very heterogeneous structure and complex hydrodynamics through conduits, fractures and matrix, therefore characteristics of groundwater flow and solute transport differ from those in intergranular and fissured aquifers. Appropriately adapted techniques of hydrogeological research are required for understanding of their functioning. This paper presents an advanced application of time series analysis in a binary karst aquifer known for its complex hydrodynamics and mixing of water from various sources of recharge. A classical approach with high temporal data resolution was extended to a spatial domain with simultaneous monitoring of precipitation, sinking streams, water flow in cave systems, and springs. The main objectives of this study were to define and compare the flow characteristics and storage capacity of selected springs and their catchments, and to determine the influence of different types of recharge (autogenic versus allogenic). The time series of recharge were analysed as input functions in the correlation and spectral analysis. The results undoubtedly show differences in water transfer through the system, storage capacity, and recharge characteristics. However, they also highlight the limitations of using cross-correlation functions to distinguish the influence of autogenic and allogenic recharge. Due to their interference, the interpretation of the results in complex karst systems can be ambiguous, therefore a method of partial cross-correlation analysis was additionally used. Although it has been used before in karst aquifers to spatially characterise groundwater circulation and autogenic recharge, in this study it was used for the first time to investigate the mutual influences of allogenic and autogenic recharge. The results confirmed that this approach provides additional insight into the functioning of binary karst aquifers.