Study region The Qilian Mountains, Northwest China Study focus Trends in flood frequency and their driving factors must be analyzed to enable the effective management of water resources in the inland rivers originating in the Qilian mountains (QMs). Based on hydrological station datasets from 12 typical rivers with annual maximum peak discharge and peaks-over-threshold (POT) flood series for the period 1970–2019, the spatial and temporal variations of flooding in 12 rivers were detected using a linear regression estimator and Mann–Kendall trend tests. New hydrological insights The results indicate that the frequency of POT floods in 12 rivers during 1970–2019 showed an increasing trend at the 90% significance level, with an increasing trend for small floods and decreasing trends for medium and large floods. Flood levels varied from east to west across the region, with an overall decreasing trend in the east, an increase in small floods in the central rivers, and significant increases in both small and medium floods in the west. Both temperature and precipitation increased after 1987, and summer precipitation was a significantly increased; as a result, POT floods in most rivers increased after the 1980 s, and trends in flood frequency showed decreases in spring and autumn and an increase in summer. The main causes of the changes in flood frequency were found to be heavy rainfall, abnormal warming, and accelerated glacial melting.