The invention is a computer implemented method for fast simulation of the flow of a single and incompressible fluid in a heterogeneous porous medium such as an aquifer or a petroleum reservoir having application such as, for example, to the development of petroleum reservoirs. After discretizing the medium with a grid, a permeability field is determined from which a diffusivity equation is directly solved in the spectral domain by an iterative procedure involving fast Fourier transforms. A first algorithm directly manages the pressures and velocities, but it may be slow for great permeability contrasts. A second algorithm, which introduces an intermediate variable updated at each iteration, allows faster processing of greater permeability contrasts than the first algorithm. The third algorithm, based on increased Lagrangian, allows consideration of infinite permeability contrasts. The algorithms allow simulation of flows in weakly to highly heterogeneous media, with a reduced computing time.