This paper presents preliminary results from two karst systems belonging to the ‘‘Jurassic Karst’’ observatory in the French Jura Mountains. The sites are characterized by localized and diffuse recharge. Physicochemical monitoring was performed at the karst outlet (springs), as well as in the unsaturated zone (cave and epikarstic spring). During two contrasting flood events, water level, temperature, electrical conductivity, dissolved organic carbon, turbidity, and dissolved oxygen were recorded at high frequency and compared. These preliminary results allow to propose a conceptual model for both sites. It was possible to distinguish specific autogenic and allogenic recharge mechanisms and to characterize the respective contribution of the saturated and unsaturated zones.