The Department of Water Resources Engineering is the natural evolution of the Wad Al-Maqbool Institute for Earth Sciences Technology. After the institute was incorporated into the higher education system of the University of Sudan for Science and Technology in the mid-1990s, it was transformed into the College of Water Sciences and Technology, offering bachelor’s degrees in Groundwater and Drilling, and Surface Water and Water Supply. Following the college's transformation from a science to an engineering program, and after consultation with various professional councils and advisory bodies, including employers, it was decided to merge the two specializations under the name of Water Resources Engineering, and the department was established under this name. The department awards a Bachelor of Science degree with honors after 10 semesters of study.

The Bachelor of Science program in Water Resources Engineering is accredited, and its graduates were recognized by the Engineering Council until 2018.

The Department of Water Resources Engineering will become a center of scientific excellence in water resources engineering, providing distinguished, first-class education and leading water research to develop water resources and serve the community in Sudan, Africa, and the world, God willing.

The department has a vision, mission, objectives, and targeted learning outcomes for each of its accredited programs. The department currently has 364 students.

The department operated on a semester system until 2007, in accordance with the examination regulations for 1996 and 2006. In 2008, the system was changed to a credit-hour system, as per the 2008 Credit Hour Examination Regulations.