Asian monsoon records are widely documented, but specific proxies of monsoonal rainfall are limited. We present here two new independent proxy records from peatland and stalagmite archives that indicate a high degree of concordance between monsoon-driven hydrological changes occurring since the last deglaciation in a broad region of central China. The wet periods elevated the water table in the Dajiuhu peatland, as recorded by reduced mass accumulation rates of hopanoids, biomarkers for aerobic microbes, confirmed by molecular phylogenic analyses. The hopanoid-based reconstruction is supported by the first report of the environmental magnetism parameter ARM/SIRM (anhysteretic remanent magnetization / saturation isothermal remanent magnetization; ratio of fine magnetic particles to total ferrimagnetic particles) in a stalagmite from Heshang Cave in central China. Heavy rainfall resulted in the enhanced transport of coarse particles to the cave and thus low ARM/SIRM values in the stalagmite. The hydrological conditions inferred from the two records reveal three relatively long wet periods in central China: 13–11.5 k.y. ago, 9.5–7.0 k.y. ago, and 3.0–1.5 k.y. ago. Archaeological evidence for the hydrological impacts on regional populations comes from the observation that temporal shifts among six distinctive cultures of the Neolithic Period to the Iron Age in central China occurred during wet periods or flood episodes. Spatiotemporal distributions of >1600 prehistoric settlement sites correlate with the proxy-inferred fluctuating hydrological conditions, with enhanced flooding risk forcing major relocations of human settlements away from riparian zones.