The integrative approach of water, energy, and food nexus (WEF nexus) is now widely accepted to offer better planning, development, and operation of these resources. This study presents a first attempt towards understanding the WEF nexus of urban environments in the Nile River Basin under conditions of hydrological droughts and fluvial floods. A case study was conducted for the capital of Sudan, Khartoum, at the confluence of the White Nile and the Blue Nile for illustration. The results were based on analyses of river flow and water turbidity data, field observations, a printed questionnaire and an interview of farmers practicing irrigated agriculture, and hydropower modelling. The study analyzes indicators for the association of river water resources environment (intra-annual regime, quantity, and quality), the status of urban irrigated agriculture, water treatment for domestic use, and hydropower generation under hydrological extremes, i.e. droughts and fluvial floods. It additionally examines the consequent interactions between the impacts on three sectors. The present study shows how floods and droughts impose impacts on the seasonal river water quality and quantity and, in turn, on the water treatment for domestic use , irrigated agriculture, and hydro-energy supply in an urban environment.The results demonstrate how the two hydrological phenomena determine the state of hydropower generation from dams, i.e. high energy production during floods and vice versa during droughts.Hydropower dams, in turn, could induce cons in the form of low fertile soils in the downstream due to retaining sediment. Finally, present and potential options to minimize the above risks are discussed.This study is hoped to offer a good support for integrated decision making on increased resource efficiency over the urban environment within the Nile Basin.