Study regionShenzhen Bay (SZB) in the east Pearl River Estuary, China Study focusEither NO3− or NH4+ is the dominant component of dissolved inorganic nitrogen (DIN) in most estuarine waters, but few studies focused on the mechanisms of ongoing DIN transformations under various hydrologic regimes. This analysis spans 31 years of DIN component changes and involves numerical simulations to identify the roles of various driving factors including runoff and biogeochemical actions. These new insights into DIN change mechanisms from the coupling biogeochemical and hydrodynamic processes would help to boost effective mitigation measures to deal with nitrate accumulation in estuarine waters, thereby supporting integrated land-ocean nutrient management. New hydrological insights for the regionThe dominant DIN component in the SZB was found to transition from NH4+ to NO3− between 1990 and 2020. Particularly in the -upper bay, there was an unexpected increase in the mean concentration fraction of NO3− in DIN, rising from 19.5% (1990‐2017) to 65.5% (2018‐2020). This change can be partially attributed to reduced runoff NH4+ inputs. Both runoff and tidal current can transport NH4+ and NO3−downstream, but the high background levels of NO3− in the lower bay contributed to sustaining NO3− in the upper bay through ebb and flow. Biogeochemical actions further strengthened the decline of NH4+ and the rise of NO3−. Even in scenarios without terrestrial source inputs, the simulated biogeochemical processes continued to help reduce NH4+ levels throughout the bay while increasing NO3− concentrations in the middle and lower bay.