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A three-dimensional (3-D) physical–biogeochemical coupled model\udwas applied to explore the mechanisms controlling the dissolved oxygen (DO)\uddynamics and bottom hypoxia during summer in the Pearl River estuary (PRE).\udBy using the numerical oxygen tracers, we proposed a new method (namely the\udphysical modulation method) to quantify the contributions of boundary\udconditions and each source and sink process occurring in local and adjacent\udwaters to the DO conditions. A mass balance analysis of DO based on the\udphysical modulation method indicated that the DO conditions at the bottom\udlayer were mainly controlled by the source and sink processes, among which\udthe sediment oxygen demand (SOD) at the water–sediment interface and the\udre-aeration at the air–sea interface were the two primary processes\uddetermining the spatial extent and duration of bottom hypoxia in the PRE.\udThe SOD could cause a significant decrease in the bottom DO concentrations\ud(averaged over July–August 2006) by over 4 mg L−1 on the shelf off the\udModaomen sub-estuary, leading to the formation of a high-frequency zone of\udhypoxia (HFZ). However, the hypoxia that occurred in the HFZ was\udintermittent and distributed in a small area due to the combined effects of\udre-aeration and photosynthesis, which behaved as sources for DO and offset a\udportion of the DO consumed by SOD. The bottom DO concentrations to the west\udof the lower Lingdingyang Bay (i.e. the western shoal near Qi'ao Island)\udwere also largely affected by high SOD, but there was no hypoxia occurring\udthere because of the influence of re-aeration. Specifically, re-aeration\udcould lead to an increase in the bottom DO concentrations by ∼ 4.8 mg L−1 to the west of the lower Lingdingyang Bay. The re-aeration\udled to a strong vertical DO gradient between the surface and the lower\udlayers. As a result, the majority (∼ 89 %) of DO\udsupplemented by re-aeration was transported to the lower layers through\udvertical diffusion and ∼ 28 % reached the bottom eventually.\udAdditional numerical experiments showed that turning off re-aeration could\udlead to an expansion of the hypoxic area from 237 to 2203 km2\udand result in persistent hypoxia (hypoxic frequency  >  80 %) to\udthe west of the lower Lingdingyang Bay. Compared to re-aeration and SOD,\udphotosynthesis and water column respiration had relatively small impacts on\udthe DO conditions; turning off these two processes increased the hypoxic\udarea to 591 km2. In summary, our study explicitly elucidated the\udinteractive impacts of physical and biogeochemical processes on the DO\uddynamics in the PRE, which is critical to understanding hypoxia in this\udshallow and river-dominated estuarine system

A numerical analysis of biogeochemical controls with physical modulation on hypoxia during summer in the Pearl River estuary