Subsurface contamination problems of metals and radionuclides are ubiquitous. Metals and radionuclides may exist in the solute phase or bound to soil particles and interstitial portions of the geologic matrix. Accurate tools to reliably predict the migration and transformation of these metals and radionuclides in the subsurface environment enhance the ability of environmental scientists, engineers and decision makers to analyze their impact and to evaluate the efficacy of alternative remediation techniques prior to incurring expense in the field. A mechanistic-based numerical model could provide such a tool. This paper communicates the development and verification of a mechanistically coupled fluid flow and reactive chemical transport under both fast and slow reactions in variably saturated porous and fractured media. Theoretical bases, numerical implementations, and modeling experiments of the model will be described. Two example problems will be presented. The first one will be a reactive transport problem to elucidate the non-isothermal effects on heterogeneous reactions. The second problem involves coupled fluid flow and reactive transport in fractured media. It purposes are to examine the effects of precipitation and dissolution on fluid flow and matrix diffusion. It would help shade some lights on the retardation ability of grain matrices on the migration of metals and radionuclides.