Molecular dynamics (MD) simulations have been coupled to valence bond/Hartree-Fock (VB/HF) quantum-chemical calculations to evaluate the impact of diagonal and off-diagonal disorder on charge carrier mobilities in self-assembled one-dimensional stacks of a perylene diimide (PDI) derivative. The relative distance and orientation of the PDI cores probed along the MD trajectories translate into fluctuations in site energies and transfer integrals that are calculated at the VB/HF level. The charge carrier mobilities, as obtained from time-of-flight numerical simulations, span several orders of magnitude depending on the relative time scales for charge versus molecular motion. Comparison to experiment suggests that charge transport in the crystal phase is limited by the presence of static defects.