In this paper, we propose a new approach to simultaneously map the fracture/conduit network and the equivalent transmissivity of the rock matrix from hydraulic head measurements acquired during pumping/injection tests in fractured aquifers. The algorithm relies on the use of a multitask neural network to directly approximate the joint inversion operator that links hydraulic head data to aquifer hydraulic properties. In which, the hydraulic head responses are used as input data while the output consists of the fracture structure and matrix transmissivity field. The multitasking is formed by fusing two single-task neural networks, both based on convolutional encoder-decoder architectures, one of which processes the fracture map inversion and the other the transmissivity map. Training neural network then relies on a large database, which consists of thousands of synthetic aquifers characterized by the presence of the fracture/conduit network and a heterogeneous transmissivity field attributed to the rock matrix, both randomly generated. In these aquifer models, the groundwater flow equation is solved in a discrete-continuum concept to numerically simulate the hydraulic head responses associated with sequential pumping/injection tests.Multitasking succeeds in reconstructing the fracture architecture and matrix transmissivity field with higher accuracy in comparison to conventional single-task networks. The difference is due to the transfer mechanism involved in the multi-task network, where the information shared between the tasks effectively enhances the accuracy of both reconstructions. However, as with other inversion techniques, the result accuracy depends on the quality and quantity of the hydraulic head data used in the inversion, as well as the prior information involved in featuring the training models.