Neonicotinoids (NEOs) are ubiquitous in global surface waters. However, the occurrence of NEOs in artificial waterways is unclear. The South-to-North Water Diversion Project (SNWDP) is the largest water diversion project in the world. Water samples from the Luoma Lake to Dongping Lake section of the Eastern Route (ER)-SNWDP were collected and analyzed for eight widely used NEOs to study their spatiotemporal distribution, ecological risks, and health risks. The total NEO concentration was 9–666, 34–138, 8–126, and 7–103 ng L−1 in the water diversion channel, Luoma Lake, Nansi Lake, and Dongping Lake, respectively. The average total NEO concentration in the water diversion channel in the dry season was twice as high as it was in the wet season, due to the precipitation dilution effect. Rather than Luoma Lake, Nansi Lake and Dongping Lake showed a seasonal difference in the average total NEO concentration. NEO concentrations in the three lakes were influenced by the inputs from natural rivers and the water diversion channels under artificial regulation. The seasonal variation in NEO composition between the water diversion channel and the three lakes suggested the channel water was not the only source for NEOs in lakes. For individual NEO ecological risks, thiamethoxam, clothianidin, and imidacloprid in the two seasons would result in high chronic risks in the water diversion channel, and moderate to high risks in Nansi Lake and Luoma Lake. Thiacloprid would result in high chronic risks in Dongping Lake in the two seasons and Luoma Lake in the wet season. For the integral NEO risks, none of the lake water sites exceeded the acute ecological threshold. Health risk assessment suggested drinking water obtained from the ER-SNWDP was safe for public health. The health risks for children exposed to NEOs from the water intake and dermal intake were higher than that for adults.