• Fluctuations in the Yangtze River and sedimentary environment control GFS evolution. • Sedimentary evolution caused unconformable distribution of groundwater age in a GFS. • Continuous uplift of discharge base level favors preservation of ancient groundwater. • Holocene fine-grained sedimentary strata led to the stagnation of regional GFS. Understanding the circulation and evolution of groundwater and its control mechanism in the Jianghan Plain, which exhibits the complex sedimentary evolution and a progressively deteriorating groundwater environment, is highly imperative and challenging to promote the practical application of groundwater flow system (GFS) and protect the groundwater resources in the region. The aim of this work was to elucidate the evolution pattern of the GFS in the Jianghan Plain and its underlying mechanism. To this end, the grain size characteristics of sediments, geochronological information, stable isotopes in clay porewater, paleoclimate indicators, and existing groundwater age were analyzed to reveal the sedimentary environment of aquifer systems at the basin scale in the study area. It was found that the sedimentary environment changed from one of deep downcutting during the Last Glacial Maximum (LGM) to a fluvial facies that was rapidly infilled with coarse-grained sediments during the last deglaciation period (LDP), and then to a stable lacustrine facies with fine-grained sediments during the Holocene warm period (HWP). These changes were closely linked to the fluctuations of the Yangtze River. Consequently, the existing GFS pattern in the basin presents an unconformable distribution of groundwater age, indicating that it results from the temporal superposition of groundwater flow controlled by the historical sedimentary environment. Dramatic sea level fluctuations since the LGM have resulted in significant changes in the water level of the Yangtze River. This process has impacted the driving force of groundwater, resulting in the evolution of the GFS from a pattern of a fully developed regional GFS during the LGM to the present pattern of a multi-hierarchy nested GFS.