In this paper we develop a Monte Carlo computer simulation model for a class of particle transport processes in flow through a porous medium. This class of problems includes transport of macromolecules in porous media, fines migration, flow of stable emulsion, deep-bed filtration and size-exclusion chromatography. The porous medium is represented by a three-dimensional network of interconnected cylindrical pores with nonuniform (possibly fractal) surfaces. The effective radii of the pores are distributed according to an experimentally-measured pore size distribution. The paths of the particles throughout the pore space are determined rigorously, taking into account the effect of various forces that contribute to the interaction of the particles with the pore space. The model can also take into account the effect of possible pore plugging, particle deposition and macromolecular adsorption on the surface of the pores, in which case such phenomena are percolation processes and are characterized by a percolation threshold which is the volume fraction of the open pores below which the medium loses its macroscopic connectivity. When the model is applied to the problem of fines migration in flow through a porous medium, the predictions are in quantitative agreement with the available experimental data.