This review addresses the growing demand for sustainable energy technologies by exploring the rapid advancements in organic dyes for aqueous-based electrochemical energy storage (AEES). By examining their functional groups, structural properties, and solvation behavior, we explore the mechanisms that govern their electrochemical behavior in aqueous environments. Organic dyes enhance interfacial charge transport via proton-electron coupled exchange. Their electrochromic behavior allows for versatile applications in AEES systems. The review systematically categorizes prominent dyes- including anthraquinone, azo, nitro, triphenylmethane, and heterocyclic compounds and highlights their redox mechanisms and electrochemical properties. Advanced analytical techniques, such as UV–Vis, Raman, FTIR, and NMR spectroscopy, provide critical insights into structure-function relationships. Investigations into aqueous solubility, ion coordination effects, and interfacial interactions emphasize the multifunctional potential of these materials. Challenges, including the irreversible transformation and shuttling effect, are addressed in dye-containing electrolytes. Additionally, the incorporation of organic dyes with conductive polymers and carbon-based additives, such as graphene and carbon nanotubes, improves charge storage and electrochemical stability. The review highlights the crucial role of organic dyes and their derivatives for AEES applications. It outlines future research directions, emphasizing the need for interdisciplinary collaboration and innovative engineering approaches to enhance their sustainability and electrochemical performance.