Water management during grain filling plays a critical role in determining rice quality, but its coordinated regulation of eating and aroma quality in aromatic rice remains unclear. In this study, two indica cultivars, Nongxiang 32 and Yuzhenxiang, were subjected to three irrigation regimes: continuous flooding (CF), alternate wetting and drying (AWD), and saturated soil irrigation (SSI). Our results showed that 2-acetyl-1-pyrroline (2AP) content exhibited the highest level under AWD and the lowest under SSI. Starch pasting properties were improved under AWD and SSI, as reflected by higher peak viscosity and breakdown and lower setback values. Further analysis of Nongxiang 32 showed that AWD enhanced amylopectin and total starch contents, elevated proline and putrescine levels, and differentially regulated enzyme activities, maintaining higher proline dehydrogenase activity at early filling stage and favorable Δ¹-pyrroline-5-carboxylate synthetase, ornithine δ-aminotransferase, and diamine oxidase activities at late filling. Meanwhile, AWD was associated with reduced γ-aminobutyric acid accumulation, consistent with greater precursor availability for 2AP biosynthesis. Antioxidant enzyme activities followed the order AWD > SSI > CF, whereas malondialdehyde and free fatty acids showed SSI > AWD > CF. Hormonal responses differed: gibberellic acid (SSI > AWD > CF), abscisic acid (AWD > SSI > CF), and indole-3-acetic acid (AWD > CF > SSI). Collectively, in Nongxiang 32, AWD optimally coordinates precursor metabolism, enzyme activities, antioxidant defense, and hormone regulation, thus improving both the aroma and starch quality of aromatic rice. This work provides a mechanistic understanding of water-driven quality formation in aromatic rice and offers a feasible irrigation strategy for high-quality aromatic rice cultivation.