Abstract Research into land subsidence caused by groundwater withdrawal is hindered by the availability of measured heads, subsidence, and forcings. In this paper, a parsimonious, linked data‐driven and physics‐based approach is introduced to simulate pumping‐induced subsidence; the approach is intended to be applied at observation well nests. Time series analysis using response functions is applied to simulate heads in aquifers. The heads in the clay layers are simulated with a one‐dimensional diffusion model, using the heads in the aquifers as boundary conditions. Finally, simulated heads in the layers are used to model land subsidence. The developed approach is applied to the city of Bangkok, Thailand, where relatively short time series of head and subsidence measurements are available at or near 23 well nests; an estimate of basin‐wide pumping is available for a longer period. Despite the data scarcity, data‐driven time series models at observation wells successfully simulate groundwater dynamics in aquifers with an average root mean square error (RMSE) of 2.8 m, relative to an average total range of 21 m. Simulated subsidence matches sparse (and sometimes very noisy) land subsidence measurements reasonably well with an average RMSE of 1.6 cm/year, relative to an average total range of 5.4 cm/year. Performance is not good at eight out of 23 locations, most likely because basin‐wide pumping is not representative of localized pumping. Overall, this study demonstrates the potential of a parsimonious, linked data‐driven, and physics‐based approach to model pumping‐induced subsidence in areas with limited data.