In this work, we describe a number of efficient and locally conservative methods for subsurface flow and reactive transport that have been or are currently being implemented in the IPARS (Integrated Parallel and Accurate Reservoir Simulator). For flow problems, we consider discontinuous Galerkin (DG) methods and mortar mixed finite element methods. For transport problems, we employ discontinuous Galerkin methods and Godunov-mixed methods. For efficient treatment of reactive transport simulations, we present a number of state-of-the-art dynamic mesh adaptation strategies and implementations. Operator splitting approaches and iterative coupling techniques are also discussed. Finally, numerical examples are provided to illustrate the capability of IPARS to treat general biogeochemistry as well as the effectivity of mesh adaptations with DG for transport.