[1] The accurate characterization of the location, hydraulic properties, and connectivity of major fracture zones is essential to model flow and solute transport in fractured media. Cross-borehole flowmeter tests, which consist of measuring changes in vertical borehole flows when pumping a neighboring borehole, were shown to be an efficient technique to provide information on the properties of the flow zones that connect borehole pairs. The interpretation of such experiments may, however, be quite uncertain when multiple connections exist. In this study, we explore the potential of flow tomography (i.e., sequential cross-borehole flowmeter tests) for characterizing aquifer heterogeneity. We propose a framework for inverting flow and drawdown data to infer fracture connectivity and transmissivities. We demonstrate that successively exchanging the roles of pumping and observation boreholes improves the quality of available information and reduces the under-determination of the problem. The inverse method is validated for several synthetic flow scenarios. It is shown to provide a good estimation of connectivity patterns and transmissivities of main flow paths. It also allows the estimation of the transmissivity of fractures that connect the flow paths but do not cross the boreholes, although the associated uncertainty may be high for some geometries.