Water crossover through the membrane of a vanadium redox flow battery system is not desirable because it floods one half-cell, diluting the vanadium solution on one side and consequently increasing the concentration of vanadium in the other half-cell. To analyze the effect of water crossover and the resultant electrolyte imbalance issue in the vanadium redox flow battery, herein we newly develop a water transport model and incorporate it into our previously developed 3D vanadium redox flow battery model. The model rigorously accounts for water production/consumption by the redox reaction of VO2+/VO2 and side reactions as well as various mechanisms of water crossover through the membrane arising from diffusion, electro-osmotic drag (EOD), and vanadium crossover. The numerical model is successfully validated against in situ data collected during experiments in which the electrolyte volumes and cell voltages are measured during charge–discharge cycles carried out under various current densities. The detailed simulation results clearly elucidate water crossover behaviors at different stages of charging and discharging, and further reveal the individual contributions of water crossover mechanisms to the overall electrolyte imbalance between the negative and positive sides of the VRFB system.