Abstract: The Farmland drainage system can be upgraded to enhance the waterlogging control capacity in the wheat growing period, particularly in the high-standard farmland construction of the rice and wheat rotation area in the plain river network region. It is also necessary to adjust the ditch and pond to fully meet the requirements of the regional drainage and mechanical operation. The drainage and pollutant output can be promoted to reduce the water purification of the ditches and ponds in the rice cultivation period. This study aims to evaluate the potential negative impact of the renovation measures. An appropriate countermeasures were also proposed, according to the 6-year monitoring data of the drainage and water quality of a rice-wheat rotation area in Yangzhou, Jiangsu Province, China. The field hydrology model-DRAINMOD was applied to determine the field drainage layout in order to fully meet the control requirements of the regional waterlogging in the wheat growing period of the high-standard farmland. There was a variation in the influence of the drainage system on the nitrogen losses in the rice growing period. Furthermore, a systematic analysis was carried out to examine the effect of the variable ditch and pond redistribution, thus considering their distribution features and hydraulic functions. Finally, the investigation was also made to explore the influence of the different distributions on the reduction of the agricultural pollutants in the ditches and ponds system. The results showed that the existing drainage ditches in the study area (with 60 cm depth and 50 m equivalent spacing) were insufficient for the required field drainage for wheat production. The required probability of 90% waterlogging control was achieved by using a 'shallow-narrow' subsurface drainage layout with the drain depth of 90 cm and spacing of 20 m, or a 'deep-wide' layout with the drain depth of 120 cm and spacing of 30 m. It was very necessary to adopt controlled drainage and Alternate Wetting-Drying irrigation in the rice growing season. The output values of the ammonia nitrogen in the field drainage were 19.23 and 18.13 kg/ha, respectively, which increased by 17.82% and 12.84%, respectively, compared with the existing drainage ditches. The existing ditches and ponds also covered 11.9% farmland area, in order to improve the drainage water quality. In the process of land consolidation, the ammonia nitrogen concentration of the paddy field drainage was kept under Class III of the surface water quality standards of China, when the ditch/field area ratio was no less than 3.8%. Therefore, the field drainage system was improved for land consolidation. Their regional distribution and water quality protection should be considered jointly; The drainage systems should be upgraded to fully utilize the local wetland resources of the ditches and ponds. A win-win situation can be achieved in food production and environmental protection.