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Water is an under-appreciated reaction medium that has been shown to facilitate photodimerization reactions. Despite having a low formal concentration, hydrophobic nature of organic compounds could lead to higher local concentrations, thereby favoring their cycloaddition. In contrast, photodimerization reactions are unlikely to occur in organic solvents under similar conditions. This study explores the supramolecular assembly of small organic molecules in water, focusing on their role in promoting photodimerization reactions. NMR spectroscopy, molecular dynamics simulations, and ab initio calculations were used to examine the dynamic interactions between indene and its aggregated state in water. Quantum mechanical calculations suggest that the stacking of indene with an antiparallel-displaced orientation is the most stable configuration, and MD simulations support the role of water in promoting aggregation. NMR results confirm the existence of indene aggregates, and 2D NMR reveals dynamic exchange between monomer and aggregate states. The study elucidates the complex dynamics of indene aggregation and its impact on photodimerization, providing insights into designing other photoreactions in water.