The Nile Basin comprises ten countries that stretch from its creation on the shores of Lake Victoria to the river. The area of the basin covers approximately 3.3 million square kilometres. The countries it crosses are Ethiopia, Sudan, Egypt, Rwanda, Tanzania, Uganda, Burundi, the Democratic Republic of Congo, Eritrea and Kenya. While most of the river`s water quality is in acceptable values, there are several hotspots, most of which are found in irrigation canals and drainages. The sources of pollution come from agricultural, industrial and household waste. There are 36 industries that dump their sources of pollution directly into the Nile and 41 into irrigation canals. These types of industries are: chemistry, electrical engineering, mechanical engineering, fertilizers, food, metal, mining, oil and soap, pulp and paper, fire, textiles and wood. There are more than 90 agricultural effluents flowing into the Nile, including industrial wastewater.  Water exceeds the minimum standards for fecal contamination, and there is high salinization and salt penetration in the delta. Salination occurs when there is a build-up of salts in the soil. The soil cannot retain water that prevents growth. Salt infiltration is when the soil is saturated with salt water.
The Northeast Nile Delta region has a high incidence rate of pancreatic cancers, which are believed to be caused by high amounts of heavy metals and organ chlorine found in soil and water. Exposure to cadmium is best known by smoking, although exposure in this region is thought to be due to contact with heavy metals and pesticides in soil and water.  Schistosomiasis (a disease caused by parasitic worms) was found in irrigation canals with benthic cyanobacteria forming mats.   Major water infrastructure projects pose a dual security threat. They can not only lead to conflicts with neighbouring countries, but also lead to internal conflicts. While dam construction can stimulate national economic growth, it is also known to have driven large communities from fertile areas of nilues to arid deserts. The Morowe Dam in Sudan, completed in 2009, has forced 15,000 families to resettle in desert areas due to forced evictions and high destructive water levels. In 2011, insufficient government compensation sparked protests in Khartoum. The Roasaries Dam, whose future expansion will significantly improve Sudan`s ability to irrigate its arable land, has also forced some 22,000 families to relocate. While these infrastructure projects are carried out with national interests in mind, the direct impact on neighbouring Nile communities can be destructive.