This study investigates Holocene sedimentary evolution and hypoxia development using borehole cores CJK06 and CJK09, in combination with other published core data. Based on lithology and microfossil (benthic foraminifera) characteristics, seven types of sedimentary facies were identified from the base upward: river, tidal flat, tide-influenced river, transgressive lag, estuary, inner-shelf, and prodelta. Isochronous correlation among the cores was established relying on accelerator mass spectrometry 14C dates. Facies succession indicates that a weak progradation occurred in coastal environments (12–10 ka BP) due to the Younger Dryas-induced deceleration of sea-level rise; rapid deposition locally occurred in the southern marginal area of tide-dominated estuary environments (10–8 ka BP), likely due to the junction of the Yangtze and Qiantangjiang River currents; and marine current-induced fluid mudflows prevailed in the shallow marine environments (8–1 ka BP), with the cooling climates of 5–1 ka BP. Furthermore, prodelta and shallow marine environments co-occurred with an uneven progradation of the delta within the last 1 ka, while deposition occurred just inside the more southern, delta-influenced area. The occurrence of euryhaline benthic foraminifera suggests that an enhanced freshwater discharge of the mid-Holocene (8–5 ka BP) was followed by a sharp decline in the late Holocene (5–1 ka BP) with climate change. The occurrence of cold-water benthic foraminifera indicates a severe cold-water condition during the mid-Holocene due to the intrusion of upwelling currents triggered by the propelling force of warm currents and summer monsoon winds. In addition, the occurrence of low-oxygen foraminiferal assemblages reveals that hypoxia has developed since 10 ka BP in stages consistent with the sedimentary evolution: localized hypoxia formation coincident with the southern depocenter during the early Holocene (10–8 ka BP); severe hypoxia with enhanced freshwater discharge and upwelling current intrusion during the mid-Holocene; and weakened hypoxia of the late Holocene, mainly due to the sharp decline in freshwater discharge. Within 1 ka BP, freshwater discharge from the approaching river mouth and increased nutrient inputs from enhanced human activities on land have contributed to the prevalence of hypoxia, especially in the southern deltaic area. Overall, it was revealed that the freshwater discharge modulated with climate variations and delta progradation plays a primary role in controlling the sedimentary evolution and hypoxia development during the mid-late Holocene. •Gravity flows (fluid mudflow) prevailed during the late Holocene (5–1 ka BP).•Holocene freshwater discharge was enhanced (8–5 ka BP) and then sharply declined.•Severe upwelling current intrusion occurred during the mid-Holocene (8–5 ka BP).•Hypoxia boomed during the mid-Holocene (8–5 ka BP).