In this study, a stress-dependent groundwater model, MODFLOW-SD, has been developed and coupled with the nonlinear subsidence model, NDIS, to predict vertical deformation occurring in basins with highly compressible deposits. The MODFLOW-SD is a modified version of MODFLOW (the USGS Modular Three-Dimensional Groundwater Flow Model) with two new packages, NONK and NONS, to update hydraulic conductivity and skeletal specific storage due to change in effective stress. The NDIS package was developed based on Darcy-Gersevanov Law and bulk flux to model land subsidence. Results of sample simulations run for a conceptual model showed that hydraulic heads calculated by MODFLOW significantly overestimated for confining units and slightly underestimated for aquifer ones. Moreover, it showed that applied stress due to pumping changed initially homogeneous layers to be heterogeneous ones. Comparison of vertical deformations calculated by NDIS and MODFLOW-SUB showed that neglecting horizontal strain and stress-dependency of aquifer parameters can overestimate future subsidence. Furthermore, compared to the SUB (Subsidence and Aquifer-System Compaction) package, NDIS is more likely to provide a more accurate compaction model for a complex aquifer system with vertically variable compression (C c ), recompression (C r ), and hydraulic conductivity change (C k ) indices.Hydrology 2019, 6, 78 2 of 17 like hurricanes, many coastal cities also experience significant land subsidence and sea level rise which both exacerbate the urban floods [5].Regional land subsidence accompanying groundwater extraction and its severe environmental consequences were reported in different locations around the world, e.g., Mexico City, Mexico [6], Beijing, China [7], Houston-Galveston, Texas, USA [8], and Santa Clara Valley, California, USA [9]. Recent worldwide measured subsidence rates for major cities that experienced substantial land subsidence showed subsidence as small as several mm/year to 38 cm/year [2,10,11].Excessive groundwater pumping declines artesian head and pore pressure in an aquifer system. Under the assumption of constant total stress, this decline causes pore water pressure to decrease and effective stress to increase. The increase in effective stress results in the compaction of compressible units within an aquifer system, including aquitards and interbeds clay lenses. As long as the effective stress remains less than the pre-consolidation stress, compaction is elastic and recoverable [12]. Increases in effective stress that exceeds pre-consolidation stress result in inelastic compaction. Inelastic compaction causes permanent deformation that cannot be recovered after unloading and diminishes the storage capacity of the aquifer system. The cumulative deformation of all compressible units is emerged on the earth surface as the land subsidence and fissures.MODFLOW, the USGS Modular Three-Dimensional Groundwater Flow Model [13], is the well-known standard model used worldwide. MODFLOW consists of a main program and different independe...