TOUGHREACT is a numerical simulation program for chemically reactive non-isothermal flows of multiphase fluids in porous and fractured media. The program was written in Fortran 77 and developed by introducing reactive chemistry into the multiphase fluid and heat flow simulator TOUGH2. A variety of subsurface thermo-physical-chemical-biological processes are considered under a wide range of conditions of pressure, temperature, water saturation, ionic strength, and pH and Eh. Reactions among aqueous species and interactions between mineral assemblages and fluids can occur under local equilibrium or via kinetically controlled rates. The gas phase can be chemically active. Precipitation and dissolution reactions can change formation porosity and permeability. Intra-aqueous kinetics, biodegradation and surface complexation have recently been incorporated. The program can be applied to one-, two- or three-dimensional porous and fractured media with physical and chemical heterogeneity. It can accommodate any number of chemical species present in liquid, gas and solid phases. TOUGHREACT can be applied to many geologic systems and environmental problems, including subsurface storage of nuclear waste and CO2, geothermal systems, diagenetic and weathering processes, acid mine drainage remediation, contaminant transport, and groundwater quality. The methods and approaches used in TOUGHREACT have been extensively published over the last decade. Here we give a general description and summary of the program, including the main features, scope, processes, and solution method. To illustrate its applicability, we present four examples: (1) Denitrification and sulfate reduction, (2) long-term fate of injected CO2 for geological sequestration, (3) bentonite alteration due to THC processes in a nuclear waste repository, and (4) chemical stimulation of an enhanced geothermal system.