The importance of the groundwater management of karst aquifers relatively to their complexity requires the knowledge of the subsurface flow and storage behavior. In this study, a methodological approach based on the exploitation of daily spring’s discharge data was developed and tested. The methodology makes use of the hydrograph recession curves, the correlograms output, and the logarithmically structured duration curves. This methodological approach was applied to the complex karst system of Louros basin. The Louros karst system consists of individual karst units discharged by respective springs which are distributed on three levels and form three easily distinguishable groups. The application results revealed a well organized karst system with conduits of slow and fast flow. It also revealed the uniformity and the complexity of the different units, as well as the properties, such as the storativity and the evolutionary process. This approach demonstrates the benefits of interpreting different methods in a hydrologically meaningful way for the recharge data evaluation.