The Lixiahe abdominal area is a representative plain river network in the lower reaches of the Huai River, being an upstream section of south-to-north water diversion from the Yangtze River in Jiangsu Province, China. The assessment of long-term water quality variation and the identification of probable causes can provide references for sustainable water resources management. Based on the monthly water quality data of 15 monitoring stations in the Lixiahe abdominal area, the periodic characteristics and tendency of water quality variation were studied by combining wavelet analysis, the Mann–Kendall trend test, and Sen’s slope estimator, and the correlation between water quality variation, water level, and water diversion was discussed with cross wavelet transform and wavelet coherence. The results show that the comprehensive water quality index (CWQI) included periodic fluctuations on multiple scales from 0.25 to 5 years. The CWQI of 7 out of 15 monitoring stations has a significant decreasing trend, indicating regional water quality improvement. The trend slope ranges from −0.071/yr to 0.007/yr, where −0.071/yr indicates the water quality improvement by one grade in 15 years. The spatial variation of water quality in the Lixiahe abdominal area was significant. The water quality of the main water diversion channels and its nearby rivers was significantly improved, while the improvement of other areas was not significant or even became worse due to the increasing discharge of pollutants. The CWQI of the main water diversion channels and its nearby rivers was inversely correlated with the amount of water diversion. The greater the amount of water diversion, the better the water quality. The water diversion from the Yangtze River has played an important role in improving the regional water environment.
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