Modern and forecasted flooding of deltas is accelerated by subsidence of Holocene deposits. Subsidence caused by tectonics, isostasy, sediment compaction and anthropogenic processes, combined with eustatic sea-level rise, results in drowning and increased flood risk within densely populated deltas. Many deltaic sedimentary successions include substantial amounts of peat, which is highly compressible compared to clay, silt and sand. Peat compaction, therefore, may contribute considerably to total delta subsidence. Existing studies are inadequate for quantifying peat compaction across deltas. We present a numerical peat compaction model calibrated with an extensive field dataset. The model quantifies spatial and temporal trends in peat compaction within fluvial-dominated Holocene flood basin sequences of different compositions. Subsidence due to peat compaction is highly variable in time and space, with local rates of up to 15 mm/yr, depending on sedimentary sequence. This is extremely important information for developing sound delta management strategies. Artificial groundwater table lowering may cause substantial additional subsidence. Subsidence due to peat compaction might even exceed estimates of relative sea-level rise, and thus, may seriously increase the risk of delta drowning and human vulnerability to flooding