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• 4R strategy for controlling AGNPS pollution was applied in Yangtze River basin. • N and P fertilizer rate reduced by 20 % and 27 % without any yield loss. • More than 40 % of N & P in the drainage was removed by eco-ditches & eco-ponds. • TN in the final field drainage was lower than 2 mg/L during 3 out of 19 times. • TN, NH 4 +-N, TP in the river decreased by 28.9 %, 30.4 %, 21.9 % after eco-restoration. Non-point pollution is becoming one of the main causes of the degradation of rural environment in China. A systematic strategy encompassing source reduction, process retention, nutrient reuse, and water restoration for controlling agricultural non-point source pollution was applied to a 1.5 km2 intensive rice-wheat rotation area at Yaoqiao county, Zhenjiang city, Jiangsu Province, in the downstream reach of the Yangtze River, China, from 2016 to 2018. The results showed that the use of organic and controlled-release fertilizers reduced the total nitrogen (TN) and total phosphorus (TP) input for rice and wheat by 20 % and 27 %, respectively, without any yield loss. The N and P concentration in the ecological ditches declined by 8%–50.4% for TN and 12%–69.7% for TP in comparison with that in the control ditches, and then further declined after the purification of eco-ponds. The removal efficiency was positive related with the N and P centration of inflow. TN concentration in the drainage water finally flow into the Shangshe River was lower than 2 mg/L during three out of 19 times. The river water quality was distinctly improved, wherein the TN, NH 4 +-N, TP, and chemical oxygen demand (COD Cr) concentrations were lower by 28.9 %, 30.4 %, 21.9 %, and 35.5 %, respectively following implementation of ecological water restoration technologies. The water quality improvement was mainly attributed to reduced pollutant load from agricultural fields and the aquatic plant uptake. This study found that the systematic "4R" approach is a promising method for decreasing the N and P loads from agricultural fields and improving the downstream water eutrophication problem, and can be extended to other agricultural intensive regions. [ABSTRACT FROM AUTHOR]