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The hydrology program began in the summer of 1900 when UC President Benjamin I. Wheeler invited Elwood Mead, head of USDA’s irrigation investigations, to organize teaching and research on irrigation. In the 1920s, members of the Division of Irrigation at Davis helped develop the California Water Plan, and a second California Irrigation map (1922). Frank Adams helped write water rights legislation. The Division became the Department of Irrigation in 1936, with a faculty of 10 under the leadership of Frank Veihmeyer.

In 1962, irrigation program faculty with engineering degrees received split appointments in either the Department of Civil Engineering or the Department of Agricultural Engineering in the newly established College of Engineering. In 1965, the department was renamed the Department of Water Science and Engineering to reflect its broadening scope.

Over the years faculty research and teaching have made outstanding contributions to the efficient development and utilization of water. Veihmeyer’s cutting edge research helped establish the departmental tradition of contributing to the basic understanding of soil-plant-water relations. With Arthur Hendrickson (Pomology), he established the now widely accepted concept of "field capacity", and the more controversial but also universally recognized concept of permanent wilting percentage. Jamie Amorocho’s hydraulic testing of structural models played an important role in the construction of conveyance and storage structures under the California Water Project. William Pruitt designed and built the largest weighing lysimeter in the world to develop basic understanding of water use by crops. His widely translated, coauthored book on crop water requirements for the Food & Agriculture Organization (FAO), United Nations (UN), serves as a universal reference.

In 1990 a campus-wide graduate program in Hydrologic Sciences was approved. The core curriculum includes courses that cut across disciplines and form the basis for specialization in areas such as ground-water contaminant transport, regional evaporation, hydrobiology and hydrogeochemistry. In addition to these areas, the current program also emphasizes teaching and research in watershed hydrology, water management, and irrigation and drainage.