This paper discusses software design choices made during the ongoing development of PFLOTRAN with the intent of improving the longevity and flexibility of the code while maintaining robustness. PFLOTRAN is a massively parallel reactive multiphase flow and transport code employed to simulate subsurface processes in support of radioactive waste management licensing and performance assessment studies. PFLOTRAN’s open source licensing, software configuration management, object-oriented design through modern Fortran 2003/2008, approach to coupling scientific process models, and automated testing are discussed in detail.