This research targets disentangling shallow causes of anthropogenically-induced subsidence in a reclaimed and urbanized coastal plain. The study area is around the city of Almere, in the South Flevoland polder, the Netherlands, which is among the countries’ fastest subsiding areas. The procedure consists of integrating synthetic Interferometric Synthetic Aperture Radar (InSAR) data with high-resolution phreatic groundwater and lithoclass models, and a database containing construction details. The two main parts of the workflow are isolation of the InSAR points of structures without a pile foundation and a data assimilation procedure by Ensemble Smoothing with Multiple Data Assimilation. The shrinkage of surficial clay beds by phreatic groundwater level lowering is identified to be the main cause of shallow subsidence in the area, with an average contribution of 6 mm/year. The history-matched physics-based model predicts that one meter drop in phreatic groundwater level now translates into 10 millimeter of subsidence in the next five years. Also, this study showed that a groundwater deficiency due to severe dry periods should be considered as an accelerator of subsidence in both the short- and long-term planning. To ensure a robust network to estimate future subsidence, we advise on a consistent monitoring strategy of the phreatic groundwater level.