The study of contaminants propagation in fractured and karstic aquifers shows uncertainties caused by the conditions of anisotropy of the medium and by the presence of cavities and residual products that could make fluid flow and solute transport unforeseeable. Therefore, in aquifers characterized by fissured and fractured solid matrix, in order to set up remediation strategies, it is necessary to represent the conditions of groundwater flow and contaminant propagation in such a way as to take into consideration the high heterogeneity connected to the presence of fractures and channels that act as preferential flow ways. In the present paper are proposed different approaches for modeling fluid flow, even in density-dependent conditions, and contaminant reactive transport.