The Nile Delta is a subsiding sedimentary basin that hosts ∼66% of Egypt’s population and 60% of the country’s food production. Projected sea-level-rise scenarios for the coming decades have sharpened focus on the delta’s potential resilience to rapid changes in accommodation space. We use chronostratigraphic data from 194 organic-rich peat and lagoon points to quantitatively reevaluate the drivers of Nile Delta surface dynamics during the Holocene. Reconstructed subsidence rates range from 0.03 to 4.5 mm/yr, and are highest in the Manzala, Burullus, Idku, and Maryut lagoons, areas that correspond to deep late Pleistocene topography infilled with compressible Holocene strata; 88% of the subsidence values are <2 mm/yr. We suggest that during the Holocene two significant but previously underestimated contributors to changes in Nile Delta mass balance have been sediment compaction and orbitally forced changes in sediment supply. Between 8000 and 4000 calibrated (cal) 14C yr B.P., spatially averaged sedimentation rates were greater than subsidence, meaning that delta aggradation was the dominant geomorphological process at the regional scale. Since ca. 4000 cal yr B.P., a sharp climate-driven fall in Nile sediment supply, coupled with the human-induced drainage of deltaic wetlands, has rendered the depocenter more sensitive to degradation by sea-level rise and extreme flood events.