Abstract: Using a nonstationary flood frequency model, this study investigates the impact of trends on the estimation of flood frequencies and flood magnification factors. Analysis of annual peak streamflow data from 28 hydrological stations across the Pearl River basin, China, shows that: (1) northeast parts of the West and the North River basins are dominated by increasing annual peak streamflow, whereas decreasing trends of annual peak streamflow are prevailing in other regions of the Pearl River basin; (2) trends significantly impact the estimation of flood frequencies. The changing frequency of the same flood magnitude is related to the changing magnitude or significance/insignificance of trends, larger increasing frequency can be detected for stations with significant increasing trends of annual peak streamflow and vice versa, and smaller increasing magnitude for stations with not significant increasing annual peak streamflow, pointing to the critical impact of trends on estimation of flood frequencies; (3) larger‐than‐1 flood magnification factors are observed mainly in the northeast parts of the West River basin and in the North River basin, implying magnifying flood processes in these regions and a higher flood risk in comparison with design flood‐control standards; and (4) changes in hydrological extremes result from the integrated influence of human activities and climate change. Generally, magnifying flood regimes in the northeast Pearl River basin and in the North River basin are mainly the result of intensifying precipitation regime; smaller‐than‐1 flood magnification factors along the mainstream of the West River basin and also in the East River basin are the result of hydrological regulations of water reservoirs.