Leakage detection and prediction of fractured rocks is an important question in hydropower engineering. Often large water reservoirs are built in karstic carbonate areas. To survey seepage of Vouglans dam (Jura, France), analysis of groundwater chemistry, according to geological conditions, is used. Statistical analysis (PCA and DFA) are used (i) to characterize more precisely the low contrast in chemical composition resulting from the interaction between surface water, groundwater and carbonate environment, and (ii) to reclassify individuals in homogeneous groups with respect to the variables studied. Three hydrodynamic behaviors were determined in the sector. The area of influence of the rapid transit of the lake water varies with the seasons, and particularly in response to changes of the water level of the lake. The hydrostatic pressure of the water column has an influence on the opening and closing of cracks at the bottom of the dam.