RT3D is a software package for simulating three-dimensional, multi-species, reactive transport of chemical compounds (solutes) in groundwater. RT3D provides an easy-to-use and flexible framework applicable to natural attenuation, accelerated bioremediation, or other reactive transport modeling scenarios. Predefined modules are available for common bioremediation scenarios, however, users have the flexibility to add any reaction kinetics desired/suitable to represent multiple chemical species in aqueous and sorbed phases. Several graphical user interfaces to RT3D are available to organize the process of defining the required RT3D input information and to provide visualization capabilities for the RT3D output. At the same time, the availability of the Fortran 90 source code provides flexibility for advanced users, regardless of the target computing platform.