The development of an organic-based aqueous redox flow battery (RFB) using quinone as an electroactive material has attracted great attention recently. This is because this battery is inexpensive, produces high energy density, and is environment friendly in stationary electrical energy storage applications. Herein, we investigate the redox potentials and solubilities of indole-5,6-quinone and indole-4,7-quinone derivatives in terms of the substituent effects of functional groups using theoretical calculations. Our results indicate that full-site substituted derivatives of indolequinone are more useful as active materials compared to single-site substituted derivatives. In particular, our calculations reveal that the substitution of -PO3 H-2 and -SO3 H functional groups with multiple polar bonds is very effective in increasing the activity of the aqueous RFB. As a strategy to overcome the limitation that the aqueous solubility is intrinsically low because they are organic molecules, we suggest the substitution of functional groups with multiple polar bonds to the backbones of active organic materials. Among 180 indolequinone derivatives, 17 candidates that meet the redox potential standards (<= 0.2 V or >= 0.9 V) and eight candidates with solubility exceeding 2 mol/L are identified. Three indolequinone derivatives that satisfy both conditions are finally presented as promising electroactive candidates for an aqueous RFB.