The accurate characterization of the underground depositional structure and hydraulic property distribution is essential to understand flow and solute transport in heterogeneous rocks or soils. Hydraulic tomography was shown to be an efficient technique to infer the spatial distribution of hydraulic properties. Due to the fact that information about the sedimentary structures’ distribution is not always available to allow a three-dimensional characterization, many of existing field applications of hydraulic tomography have been limited to two-dimensional imaging along horizontal layer or vertical profiles where hydraulic data were collected.In this work, we explore the potential of combining tomographic pumping and flowmeter tests responses in an inverse approach for three-dimensional aquifer characterization. The tomographic pumping data provide information about the lateral hydraulic connections between boreholes, while the flowmeter data constrain the vertical heterogeneity structure. The inverse approach is first validated using two synthetics models composed of multi-layered depositional structures and heterogeneous hydraulic properties within each layer. It is shown that adding the information provided by the flowmeter profiles, the inverted model exhibits more realistic depositional features. We then apply the proposed approach to characterize the 3D hydraulic conductivity field controlled by sedimentary structure of an experimental site in layered porous rocks. The inverted hydraulic conductivity field is in a good agreement with permeability measurement on drilled cores. The proposed method offers an efficient and low-cost approach for rapid assessment of the hydraulic properties in 3D and could be extrapolated to other field applications.