The transition to use more renewable energies is essential to mitigate climate change and to reduce the dependency on fossil fuels. However, the intermittent nature of solar and wind energies requires more efficient and scalable energy storage systems to ensure a reliable energy supply at demand. Flow batteries and particularly aqueous organic flow batteries, have emerged as a promising solution for stationary storage applications due to their inherent fire safety and more importantly due to their ability to decouple energy and power. Unlike traditional vanadium-based flow batteries, aqueous organic flow batteries utilize redox-active organic molecules that are attractive for their potential for low cost and synthetic tunability. In this thesis, we took two approaches towards the development of aqueous organic flow batteries. First, we studied the electrochemical properties and flow battery performance of two novel functionalized naphthalene diimides focusing on their solubility, redox behaviour and stability in the battery. Second, to address the self-association behaviour of organic molecules with aromatic cores, we studied the effect of adding a chaotropic agent such as urea to the battery electrolyte to see if it improves the accessible concentration of active material and enhances the capacity utilization of the battery. Although reduction in aggregation was observed in NMR, this did not affect capacity utilization in the flow battery. Together, these studies provide a valuable understanding on how the structure of the redox-active molecules influence the electrochemical performance and stability of the flow battery.