On the edge of sedimentary basins, karst aquifers can be fed by several water origins from both autogenic and allogenic recharge. In some cases, water origin assessment is difficult and issues in water management may arise. The main goal of this study is to understand what controls hydrodynamical and geochemical variations at the outflow of a quite complex and large karst system. More precisely, this study illustrates how a consistent observational setup can be developed, based on a multi-proxy approach that can be used for tracing water origins, evaluating mixing phenomena, and contributions in karst aquifers considering both autogenic and allogenic recharge. The Ouysse karst system (650 km2), located in western France, provides the opportunity of studying water-mixing processes in binary karst systems fed by allogenic and autogenic recharges. Global water chemistry, hydrograph and chemograph analysis during a flood event, and source-mixing calculation were used to evaluate groundwater-flow origins and the contribution of each water type during the studied flood event: (i) karstic water; (ii) evaporite water; (iii) water from igneous-metamorphic rock aquifers. In terms of resource management, the information obtained can be used as a basis of forecasting and management actions.