PFLOTRAN User manual: A Massively Parallel Reactive Flow and Transport Model for Describing Surface and Subsurface Processes. PFLOTRAN is an open source, state-of-the-art massively parallel subsurface flow and reactive transport code. PFLOTRAN solves a system of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops. Parallelization is achieved through domain decomposition using the PETSc (Portable Extensible Toolkit for Scientific Computation) libraries. PFLOTRAN has been developed from the ground up for parallel scalability and has been run on up to 2^18 processor cores with problem sizes up to 2 billion degrees of freedom. PFLOTRAN is written in object oriented, free formatted Fortran 2003. The choice of Fortran over C/C++ was based primarily on the need to enlist and preserve tight collaboration with experienced domain scientists, without which PFLOTRAN’s sophisticated process models would not exist.The reactive transport equations can be solved using either a fully implicit Newton-Raphson algorithm or the less robust operator splitting method.