A comprehensive analysis of the effects of major climate conditions such as El Nino Southern Oscillation (ENSO) and precipitation on changes in runoff and sediment transport in a basin may provide a scientific basis and technical support for regional water resource management and protection of the aquatic ecology. Taking the Taojiang River as an example, a large set of hydrogeographic data on runoff and sediment transport measured on a monthly basis from 1957 to 2015 was analyzed to study the impacts of various correlation factors on runoff and sediment transport in the river, which is located in the middle and lower reaches of the Yangtze River. Besides the conventional Mann–Kendall (M-K) method, cross-wavelet and wavelet coherence analysis methods were also applied in the data analysis. The results showed that: (1) From the M-K mutation tests conducted for the runoff volume and the sediment transport rate from 1957 to 2015, there were no significant changes in runoff. However, a mutation occurred in the sediment transport rate in 2005 and the average annual decrease reached 88.2237 million tons. (2) Precipitation was a dominant factor that controlled the changes in runoff volume and sediment transport rate. It directly influenced the changes in runoff volume, which subsequently caused the changes in sediment transport rate in the study area. Since the year 2005, sediment transport rates have been heavily influenced by the construction of large-scale hydro-power stations (Julongtan), causing a significant rate decline. A comparison between the sediment transport volume during 2005 to 2015 and that during 1980 to 2004 revealed that the annual sediment transport decrease reached 84.4079 million tons, accounting for 95.7% of the total decrease in sediment transport volume. (3) The significant resonance cycle between the sea surface temperature (SST) and the precipitation, runoff volume and sediment transport mainly occurred with a cyclic period between 1.33 and 5.33 years. During an ENSO event, the precipitation, runoff, and sediment transport rates all decreased at the beginning, then increased and reached their maximums, followed by a decline at the end.
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