Reactive molecular dynamics simulations are performed to study proton transport in various aqueous systems. Methods such as ab initio molecular dynamics (AIMD) simulations, experiment directed simulations of AIMD (EDS-AIMD), and the multistate empirical valence bond (MS-EVB) methods are used to capture both normal diffusion and the bond rearrangement of the Grotthus mechanism. Work is presented that focuses on correlating information from MD simulation to recent nonlinear spectroscopy experiments, investigates the influence of external electric fields on proton transport in the Nafion proton exchange membrane, improves AIMD water simulations by using EDS, and investigates the proton hopping mechanism is AIMD simulations. EDS-AIMD and MS-EVB simulations provide reorientation time constants that correspond to the special-pair dance – a process where the special-pair changes in the distorted Eigen cation – in addition to irreversible proton transport. The time constant of irreversible proton transport are further analyzed as a function of concentration and temperature to provide molecular support to recent experiments which showed that counter ions create entropic barriers to proton transport. The self-consistent iterative MS-EVB method show that external electric fields enhance the dynamical properties of proton in the Nafion membrane, while showing that protons transport via the potential energy well around sulfonate groups – as shown by previous reactive simulations. The EDS method was used to bias the hydrogen bond in AIMD water simulations that produced structural and dynamical properties close to the accurate MB-pol. Lastly, the proton hopping mechanism in AIMD simulations were reanalyzed that showed single hops are the dominate hopping mechanism, which is in contrast to recent AIMD studies that showed that double hops dominate. Taken together, these studies show how various reactive molecular dynamics simulation methods can investigate proton transport in aqueous systems.