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The history of the organization was divided into two systems as figure illustrated:
The left system named central water agencies from 1946 to 2002. In 1946, the Ministry of Water Conservancy, was reduced and merged into Water Conservancy Agency, MOEA in 1948. By the curtailment, the Water Conservancy Department was set up in 1949. Through the merger and formation, the Water Resources Bureau, MOEA was created in 1996.

The right system named Provincial Water Agencies. In 1947, through the reorganization of the Irrigation Conservancy Bureau, Department of Agriculture and Forestry, TPG and partly merger of the Public Construction Bureau, Department of Construction, TPG into the Water Conservancy Bureau, Department of Construction, TPG. In 1997. by the streamlining of provincial government, the Water Conservancy Agency, MOEA was created through the combination of the Water Conservancy Department, TPG and merger and formation of the Shihmen Reservoir Administration, the Liyutan Reservoir Administration and the Tsengwen Reservoir Administration.

The Water Resources Agency, MOEA was created in 2002, which combined a few former agencies such as the Water Resources Bureau, the Water Conservancy Agency, and the Taipei Water Resource Specific Committee, into one new unit named Water Resources Agency, MOEA, with the objective of promoting higher administrative efficiency among the water-related MOEA agencies, and strengthening the related business functionality.