He was made a judge in Jiujiang afterwards and became the inspecting censor of Guangdong, director of education for Beizhili, and undersecretary in the Grand Court of Judicial Review.
Later, he was appointed Right Assistant Censor-in-Chief and then Director-General of the Grand Canal (總理河道, zongli hedao), but he was soon obliged to resign to mourn his mother's passing.
He returned to the position in 1570 and built a low dyke (縷堤, lüdi) from Xuzhou to Pizhou that incurred criticism for hindering the traffic in tribute grain.
Before this was undone in 1588, he expanded the Han-era Gaojia Weir (高家堰, Gaojiayan) first constructed by Chen Deng, attempting to use the Huai to clear the silt of the Yellow River which then flowed south into Hongze Lake.
As Director-General of the Grand Canal in 1572–1574, Wan Gong's solution for the Grand Canal and the Yellow River was building dyke to confine and narrow a section of the watercourse, increasing the velocity of the current ensued and causing the current with higher velocity to carry more silt so that the watercourse would discharge silt into the sea.