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Based on the data of meteorological and hydrological collected from 1961 to 2004, the cause have been analyzed on the lowest runoff in the upper reaches of yellow River in recent years in this paper. The results indicate runoff recorded exhibited slight decrease trend from 1961 to 2004, but there is a notable decrease trend of runoff since 1990. It is noteworthy that low stream continued 15 years from 1990 to 2004, besides 1993 and 1999. Moreover, 9 year amount of runoff anomalous percentage below - 30% among 13 years of the low runoff years , account for 69%, contrast to 6.5% from 1736 to 1998. The paper has discussed the cause of the persistent low flow in the upper reaches of Yellow River in recent years based on the data of general circulation of atmosphere, sea-surface temperature(SST), sensible heat flux over Tibetan Plateau, precipitation, temperature, wind speed, sunshine time, amount of evaporation and maximum depth of frozen ground since 1990. The main cause is showed to be persistent low precipitation since 1990, which may be caused by NAOI maintained positive height phase in winter, East Asian big trough leaning depth, West Pacific Ocean subtropical high pressure ridge line position near southerly, greater sensible heat flux in spring and summer over Tibetan Plateau and stronger geothermal fields that easily result in a kind of typical Northwest drought circulation of 500hPa south positive and north negative, west positive and east negative, weak north wind and strong west wind, and deep East Asian trough and strong Xinjiang ridge in summer in East Asian. Secondarily, the reduction of rainy days above 5 mm and steady rainy days, higher temperature and larger evaporation in spring and summer is disadvantageous to create runoff. The results also indicate that the drought of the surface in the basin resulted in the decreasing trend of the runoff.