隆慶元年，為資引黃河水濟助河漕（徐州城至淮安府城間的運道），將黃河下游導向東行，匯成單一河道，從安東縣雲梯關入海。從此徐州城至淮安府城間6百餘里的運道，既是黃河也是運河。為避免糧船北上，西溯黃河，遇上伏、秋洪汛，而遭覆滅；隆慶六年六月，萬恭重新議訂漕運北上行程：江南糧船最遲不得超過三月過淮河，因此在徐州城轉入山東運道的時間，不會遲於四月。如此，江南糧船須提早於前年的冬季開船，以利明年四月以前行經黃河進入山東運道。但此時正值冬春枯水期，況長江潮水也低落，為使糧船能順行北上，萬恭須整治缺乏河水量的鎮江運河，及航行困難的瓜洲河。鎮江運河長約300里，位在岡身上，於春夏二季，其能通行糧船，主要是接引江潮。現在江南糧船須於十二月啟航，為因應江潮低落，萬 恭主要採行如下方法：（一）濬深此段運道，而後引運河水北流，以灌注 京口一帶運道通航所需的水量。（二）為加強維護江南運河，建請設置江南管河郎中。瓜洲河長30里，其能通行糧船的水量，主要來自高郵、寶應等湖往南流的湖水。因此為防範運河水南洩於大江，瓜洲河須設置11座車船壩，以節蓄運道水量。但糧船盤過水壩甚為艱難，為能順利經行，其盤壩時，需乘湧漲的江潮。晚明，黃、淮二河水入灌高郵、寶應等湖，各湖水勢盈盛。此時水文的改變，若瓜洲壩河能改建為船閘，已無先前有傾洩運河水的疑慮。因此，隆慶六年八月萬恭建造瓜洲閘河，此項工程：（一）開鑿花園港運道，長6里。（二）運道上建置船閘2座。萬恭為因應黃河全流東行，在漕河所整建的各項工程，其能維持長久者，僅瓜洲的花園港閘河；至於濬深鎮江運河，則未能產生長期效用。

In 1567, in order to direct water from the Yellow River to support the channel (canal between Xuzhou and Huaian), the downstream of Yellow River was directed eastward, aggregated into a single river channel and drained into the sea at Yunti Pass of Andong County. From then on, the 600 mile canal between Xuzhou and Huaian was not only the Yellow River but also a canal. To prevent capsizing of northbound or westbound grain boats on the Yellow River encountering summer and autumn floods, in June 1572, Wan Gong again established the northbound freight schedule: Jiangnan grain boats may not pass the Huai River later than March, so that they turn to the Shandong canal in Xuzhou no later than April. Therefore, Jiangnan grain boats must set out during winter of the previous year in order to enter the Shandong canal via Yellow River before April of the following year. However, during the winter and spring waters were low, as was the Yangzi River. To enable the smooth northbound travel of grain boats, Wan Gong had to modify Zhenjiang Canal, which was lacking in river water and Guazhou River, which was difficult to navigate. Zhenjiang Canal was about 300 miles long, located on hills. In the spring and summer, grain boats could pass because river tides were connected. At the time, Jiangnan grain boats must set sail in December, in response to low river tides, Wan Gong used the following methods: (1) deepened this section of the canal, and direct northward flow of the river to inject water required for navigation in the Jingkou region. (2) An official position managing the river at Jiangnan was established to improve maintenance of the Jiangnan Canal. Guazhou River was 30 miles long, and its water allowing for navigation of grain boats primarily came from lake water flowing southward from Gaoyou and Baoying lakes. To prevent the canal's southward leak into the river, 11 waterway dams had to be established on Guazhou River to save canal water volume. However, it was difficult for grain boats to overcome the dams. To enable smooth passage, dam passage must rely on rising river tides. In late Ming, water from Yellow and Huai rivers flowed into and filled Gaoyou and Baoying lakes. At this point, there were changes in hydrology; if Guazhou dams could be reconstructed into navigation locks, then there would no longer be concern about torrential release of canal water. Therefore, in August 1572, Wan Gong constructed Guazhou Zha River, in which: (1) the 6-mile Huayuangang Canal was dug; (2) two navigation locks were constructed on the canal. In order to cope with eastward flow of Yellow River, among the constructions by Wan Gong on Cao River, only Huayuangang Zha River of Guazhou could be maintained in the long run; deepening of Zhenjiang Canal did not result in long-term efficacy.