AbstractRiver floods influence sedimentary environments and ecosystems from the terrestrial to the deep‐marine. This study documents the occurrence conditions of hyperpycnal flows generated by river floods and related organic‐matter sedimentation for Holocene sediments of the Niigata Plain, Central Japan, based on detailed sedimentary facies, total sulfur and total organic carbon content, diatom assemblages and organic‐matter composition. Holocene sediments of the Niigata Plain consist of sand, mud and gravel that were deposited in estuarine and fluvial systems during a sea‐level rise (15 000–6800 years BP) and stillstand (after 6800 years BP) following the Last Glacial Maximum. Hyperpycnites are present in the upper part of the estuarine lagoon sediments. The depositional age is considered to be about 5000 years BP. The hyperpycnites comprise two successions of a top fining‐up unit and a basal coarsening‐up unit, and include abundant terrigenous organic matter and freshwater diatoms. A large volume of freshwater is inferred to have flowed into the lagoon during deposition of the upper part of the lagoon sediments. In consequence, hyperpycnal flows may have readily formed in the lagoon, because the halocline was weak. The hyperpycnal flows also produced a layer of concentrated terrigenous organic matter in the uppermost part of the hyperpycnites. The abundant organic matter on the estuarine floor is inferred to have produced anoxic bottom conditions owing to oxidative decomposition by benthic bacteria.