The variety of water-related problems in Egypt requires specialization in many different fields. The Center has therefore established twelve research institutes that read like a list of problems facing Egypt's irrigation sectors. These are:
1.Water Management & Irrigation Research Institute (WMRI)
2.Drainage Research Institute (DRI)
3.Water Resources Research Institute (WRRI)
4.Nile Research Institute (NRI)
5.Hydraulics Research Institute (HRI)
6.Channel Maintenance Research Institute (CMRI)
7.Research Institute for Groundwater (RIGW)
8.Construction Research Institute (CRI)
9.Mechanical and Electrical Research Institute (MERI)
10.Survey Research Institute (SRI)
11.Coastal Research Institute (CORI)
12.Environment and Climate Research Institute (ECRI)

ALSO
The Center includes three general administrative departments:
1. Planning and follow-up Department.
2. Research Services Department.
3. Administrative and Financial Department.

Besides the following special units:
1. Strategic Research Unit (SRU)
2. Central Laboratory for Environmental Quality Monitoring (CLEQM)
3. Information / Documentation Center
4. Central Library
5. GIS Unit
6. Gender Equality Unit
7. Printing and Publishing facility.