Coastal-prism sediments record rising local water levels, forced by sea-level rise. Sea-level rise is the primary driving factor, but the anatomy of the coastal prism is a result of a complex interplay of sea level, subsidence, and upstream controls (essentially sediment load). The sedimentary architecture of a coastal prism is linked to paleo–groundwater rise. Groundwater rise is quantified for the entire Rhine–Meuse delta (extending 120 km inland, 60 km wide) between an 11.0 kyr BP groundwater lowstand and the present highstand, dating series of organic markers (peats) of paleo–groundwater levels at compaction-free locations. The accumulated dataset of paleo–groundwater-level markers (> 300 index points) has a dense spatial and temporal coverage and a predictive quality that enables geostatistical analysis. The combination of this dataset and a carefully designed interpolation method (a form of 3D kriging) reveals the interplay between upstream (climate, discharge) and downstream (sea level, tides) controls on gradients of groundwater level and patterns of groundwater rise. Regional effects due to local controls (differential subsidence, groundwater flow) are also identified. It is shown that backfilling of the paleovalley continues into the late Holocene, when eustatic rise had ceased, while at the same time the delta is prograding in the backbarrier area. The results corroborate earlier results regarding differential subsidence and postglacial enhanced subsidence rates (relative to long-term background rates) in the delta. Moreover, the 3-D geostatistical interpolation opens possibilities to test and further develop process-based models for deltaic deposition