Groundwater, the planet’s largest active freshwater resource, plays a critical role in sustaining ecosystems, economies, and societies. Over the past two decades, China’s groundwater regulation policies have significantly elevated groundwater levels (GWLs) in many regions. However, some areas have experienced unexpected or anomalous GWL declines unrelated to groundwater extraction. The purpose of this study is to investigate the causes of anomalous groundwater dynamics processes in a coastal multilayered aquifer in Pinghu city, China. By leveraging multi-source satellite data analyses, including GRACE, InSAR, and isotope techniques, this study identified that leakage within groundwater systems and changes in precipitation, evapotranspiration were the primary drivers of groundwater storage (GWS) reduction across all monitoring stations in Pinghu City, China. The Random Forest model yielded the highest accuracy (R2 = 0.72, CC = 0.85, RMSE = 0.11) among the three downscaling methods. A strong correlation (around 0.75) is observed between GWS changes and meteorological variables. The Hongni (HN) station, which monitors multiple deep confined aquifers, was particularly sensitive to GWS fluctuations. To interpret these dynamics, a conceptual model was developed to characterize the interactions within the multi-layered aquifer system, consisting of both unconfined and confined aquifers separated by leakable aquitards. The layered aquifer-aquitard structure observed in Pinghu City is a characteristic feature of coastal and alluvial depositional systems globally. The developed conceptual model was also proven to be effective in the coastal multilayered aquifer in Texas, USA. This model offers a valuable framework for investigating groundwater dynamics in coastal plains with analogous geological settings. The analysis further revealed a temporal effect of key factors influencing the response of deep aquifers, providing critical insights into the mechanisms driving changes in deep groundwater systems
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