The Yellow River, China, experienced >1000 levee breaches during the last 3000 years. A reduced-complexity model is developed in this study to explore the effects of climate change and human activity on flood levels, levee breaches, and river avulsions. The model integrates yearly morphological change along a channel belt with daily river fluxes and hourly evolution of levee breaches. Model sensitivity analysis reveals that under natural conditions, superelevation of the channel belt dominates flood frequency. When there is significant human-accelerated basin erosion and breach repair, the dominant factors shift to a combination of mean annual precipitation, superelevation, critical shear stress of weak channel banks, and the time interval between breach initiation and its repair. The effect of precipitation on flood frequency is amplified by land use changes in the hinterland, particularly in the erodible Loess Plateau. Uncertainty analysis estimates the most likely values of the dominant factors for six historical periods between 850 B.C. and A.D. 1839, which are used to quantitatively reconstruct flood dynamics. During 850 B.C. to A.D. 1839, when the sediment load increased fourfold, the breach recurrence interval was shortened from more than 500 years to less than 6 years, and the breach outflow rate increased~27 times. River management practices during A.D. 1579 to A.D. 1839 focused on levees and triggered a severe positive feedback of increased levee heights and flood hazard exacerbation. Raising the levee heights proved to be ineffective for sustainable flood management.