The building of the ponds and canals under the management office was started about 200 years ago during the reign of Qing Dynasty Emperors Qianlong and Jiaqing (1736-1816). This was jointly funded by local people or individual investment and many were built sequentially due to irrigation needs. However, during the Japanese colonial period, farmland irrigation projects that were originally used mainly for private profit were re-designated public projects, with ponds and canals assigned for public use classified as “public ponds and channels” and subject to the guidance and supervision of government officials. In 1923, the mandatory public ponds and channels were transformed into more autonomous Irrigation Cooperatives. However, by the end of World War II (1945), farmland irrigation facilities were destroyed and in dire need of repair and the government, while conducting a program of comprehensive repairs, reorganized the Irrigation Cooperatives into Irrigation Coordination Associations, a cooperative farmers group.

In February 1948, in order to boost rural economic benefits and expand farmers' interests, Taiwan Provincial Government merged the Irrigation Cooperatives and Flood Control Associations and reorganized them as Irrigation Committees. On January 19, 1955, a Presidential Decree amended Paragraph 2, Article 2, of the Water Act "The authority-in-charge may, taking into account local needs, grant approval for setting up local irrigation autonomous organizations to promote irrigation works in conformity with government policy." Paragraph 3 stipulates that the farm irrigation association referred in the preceding paragraph shall be a public juristic person. The provincial government drafted the "Improving Measures and Organizational Charter of Irrigation Committees of Taiwan Province" in accordance with the revised provisions. In October 1956, the office was renamed Taiwan Province Tamsui-Keelung Irrigation Association and held elections to choose member representatives and a president.

From November 1956 to December 1973, the operations of the Irrigation Association became increasingly difficult, leading to proposals for its improvement and restructuring. On September 26, 1974, Taiwan Provincial Government announced, "Guidelines for the Improvement of Irrigation Associations during the Period of Accelerated Rural Construction in Taiwan Province." The 22 water conservancy associations of the province were adjusted and integrated into 15 units, and the Irrigation Associations of Tamsui and Keelung were also merged into the Taiwan Province Peikee Irrigation Association. During this period, elections of member representatives were suspended, and the president was appointed by the provincial government.

On March 27, 1982, the “Organizational Charter of the Taiwan Provincial Irrigation Association” was announced, the implementation of farmland irrigation improvement was ended, and the election of member representatives was restored with the president elected by member representatives.

When the government revised the general organizational rules for Irrigation Associations on June 1, 1994, an advisory committee and president were appointed until May 31, 2002. At that time, the general organizational rules of the Irrigation Association were again revised. The president was once more elected by all members and the advisory committee elected by all members by district, with those elected serving a four year term in office.

◎Former Tamsui Irrigation Association:

• 1922, Established as the "Taipei Prefecture Public Irrigation Canal Cooperative."
• March 31, 1923, Divided into five Irrigation Cooperatives: Longquan, Datun, Jinquanji, Chengqu, and Balian.
• January 31, 1883, Merged into the Tamsui Irrigation Cooperative
• May 1946, Renamed Tamsui Irrigation Coordination Association.
• February 1948, Renamed the Tamsui Irrigation Committee.
• October 1956, Re-designated Taiwan Tamsui Irrigation Association.

◎Former Keelung Irrigation Association:

• 1920, Established as the Taipei Prefecture Public Irrigation Canal Cooperative.
• 1922, Divided into 36 Irrigation Cooperatives including Jinshan, Wanli, Qidu, Dingda, Baxihou, Ruifang and Pinglin.
• 1938, Merged into Keelung Irrigation Cooperative.
• November 1946, Renamed Keelung Irrigation Coordination Association.
• February 1948, Renamed Keelung Irrigation Committee.
• June 25, 1954, Water Resources Bureau took over and became Keelung Irrigation Management Office.
• October 1956, Re-designated Taiwan Province Keelung Irrigation Association.

• January 1, 1975, Irrigation Associations of Tamsui and Keelung are merged into the Taiwan Province Peikee Irrigation Association, with the president appointed by the provincial government.
• June 1, 1982, Government administration ends and the election of member representatives is resumed, with the president elected by member representatives.
• June 1 1994 to May 31, 1998, Government revises the general organizational rules of the Irrigation Association and appoints the first president and advisory committee.
• June 1, 1998 to May 31, 2002, Second appointed president and advisory committee manage the Irrigation Association.
• June 1, 2002, Government revises the general organizational rules of the Irrigation Association resulting in the first directly elected president and advisory committee with a four-year term.
• May 2006, Second directly elected president and advisory committee take office.
• May 2010, Third directly elected president and advisory committee take office.
• January 1, 2013, Renamed Taiwan Peikee Irrigation Association with the approval of the Council of Agriculture, Executive Yuan.
• May 2014, Fourth direct election for president and advisory committee are held, taking office on June 1, 2014.
• October 1, 2020, Restructured as the Peikee Management Office of the Irrigation Agency, Council of Agriculture, Executive Yuan.
• August 1, 2023/8/1 Restructured as the Peikee Management Office of the Irrigation Agency, Ministry of Agriculture.