This work presents the development of an integrated system for the threedimensional modelling of flow and transport in porous and fractured media. The system is composed of six computational programs, which are responsible for the generation of geologic surface (Gocad), generation of fracture network (FracGen3D), geometric modelling (MG), numerical analysis of flow and transport (solute and particles) (FTPF-3D) and results visualization (Pos3D and Matlab). Of the programs, two had been developed in this work (FracGen3D and the FTPF-3D) and four had been integrated to the system (Gocad, MG, Pos3D and Matlab). The system is able to model the porous, fractured, fractured porous media (porous and fractured medias interposed) and a combination between the media. In the fractured or fractured porous media, the fractures generated can be of the type deterministic and/or statistical. The characteristics of the statistical fractures can be generated according to probabilistic distributions or with constant values. The numerical analysis program uses the Finite Element Method to solve the governance equations, considering steady-state and transient flow, in saturated and unsaturated conditions. For the solution of non linearity of the flow equation, the Picard scheme or the BFGS scheme are adopted. In the solute transport, the advection, dispersion, diffusion, sorption and decay mechanisms can be considered. This work also presents numerical examples used in the validation of the carried through computational implementations and other examples used to demonstrate the system that has been developed.