Aqueous organic redox-flow batteries have emerged as promising candidates for the low-cost long-duration energy storage solution that is required to integrate renewable energy into the electricity grid. However, their widescale deployment is currently limited by crossover of redox-active material through the separator membrane, which leads to capacity decay over time. Traditional membrane permeability measurements only account for diffusional crossover, and do not capture all contributions to membrane transport in working batteries, including migration. Here we present a new method for characterising crossover in operating aqueous organic redox-flow batteries, using on-line 1H NMR analysis. Using the 2,6-dihydroxyantharquinone/ferrocyanide battery as a model, we observed a doubling of 2,6-dihydroxyantharquinone crossover rates during battery charging, which we believe is due to additional transport by migration. This method can distinguish different transport mechanisms during battery charging and will aid the optimisation of charging protocols and membrane design in the future.