In recent years, water needs increased, driven by climate change and world population growth. In this context, we study groundwater flow in the vadose zone of Beauce aquifer (O-ZNS site, France). This lacustrine limestone vadose zone is characterized by multi-scale heterogeneities. They are defined by strongly various pore structures. This leads to uncertainties for reservoir properties prediction using geophysical methods which impacts reservoir models for flow simulations. In this study, we combined microstructure description and petrophysical analysis in order to model and predict reservoir properties based on different limestones facies and to infer the influence of weathering/fracturing on both acoustics and electrical properties. A total of 16 samples from these facies were cored and characterized by their porosity, permeability, acoustic velocities, complex electrical properties and microstructure analysis. Based on our multi-method approach, we demonstrated the influence of rock structure on reservoir properties prediction and modelling. Petrophysical and microstructure characterization have highlighted two main facies (microporous and homogenous facies and macroporous and heterogenous facies) which can be used to improve reservoir and flow models. However, further development is needed in order to quantify macropores and their link with weathering and to assess permeability models using electrical properties.