The College of Water and Environmental Engineering began in its initial form as a training centre for groundwater well drilling in 1962. Technicians were trained, leading to the Sudaneseization of the drilling profession. In 1968, the first batch was admitted under the name (Wad Al-Maqbool Institute for Drilling Engineering). In 1970, the second cohort specializing in water well drilling and the first cohort specializing in surveying and hydraulic drawing (surface water) were admitted. In 1974, a cohort from the Southern Region was admitted under a two-year program. The institute's name was changed to the Wad Al-Maqbool Institute for Groundwater Technicians in 1976, and it comprised four departments offering a three-year diploma:

(a) Groundwater Well Drilling Department

(b) Surveying and Hydraulic Drawing Department

(c) Groundwater Research Department

(d) Water Station Installation and Network Connection Department

In 1994, the institute was incorporated into the Sudan University of Science and Technology (Faculty of Earth Sciences), and its name was changed to the Faculty of Water Science and Technology, offering a Bachelor of Science degree in Water Science and Technology with two specializations:

(a) Surface Water and Water Supply

(b) Groundwater and Drilling.

The first cohort of Bachelor of Science students was admitted for the 2000-2001 academic year. In 2006, the college was transformed from a College of Science to a College of Engineering. The Groundwater and Drilling specialization and the Surface Water and Water Supply specialization were discontinued, and two new programs were approved:

(a) Water Resources Engineering.

(b) Environmental Engineering.

In 2007, the college's name was changed to the College of Water and Environmental Engineering. Admission to the college was initially limited to the Water Resources Engineering department until 2007. In 2008, the first cohort of Bachelor of Science students in Environmental Engineering were admitted by the General Administration of Admissions.

The Water Resources Engineering program was recognized by the Sudanese Engineering Council in its meeting (Resolution No. 8/11/104) dated April 24, 2008 (Engineering Council Resolutions 2008).

The recognition of both the Water Resources Engineering and Environmental Engineering programs was renewed by the Sudanese Engineering Council in its meeting No. (26) dated August 25, 2013 (Engineering Council Resolutions 2013).