Nitrite serves as a key intermediate in the nitrogen cycle, with its microbial-driven cycling regulated by various environmental factors. However, how nitrite cycling responds to changing environmental conditions remains unclear. Here, we address this question by integrating natural abundance stable isotope techniques with geochemical modeling in China’s largest estuary—the Changjiang (Yangtze River) estuary—and its adjacent coastal waters, a dynamic hotspot shaped by strong anthropogenic and natural forces. From summer to autumn, shifts in water column structure—from stratification and hypoxia to mixing and reoxygenation—significantly regulate nitrite dynamics. Nitrite sources exhibit unexpected consistency across seasons, despite oxygen fluctuations from hypoxia to reoxygenation. Conversely, nitrite sinks exhibit clear seasonality and vertical structuring that are closely associated with transitions between stratification and mixing. Active nitrite oxidation is confirmed in the coastal seasonal hypoxic zone, with no clear evidence supporting the occurrence of enzymatic nitrate/nitrite isotopic exchange reaction. These findings advance our understanding of how coastal nitrogen cycling responds to seasonal environmental variability and provide a transferable framework for improving predictions of biogeochemical feedbacks under intensifying stratification and deoxygenation in a changing climate.