This study was conducted to assess the impacts of water stress on diurnal photochemical efficiency of PSII and morphology of seedlings of A. senegal from two different provenances (El Fasher, P1 and Buram, P2). Seedlings were grown at the nursery of the Department of Forestry and Range Sciences, University of Al-Fashir, North Darfur, Sudan. Fifty four seedlings per provenance were selected and divided into well-watered (W) and water-stressed (D) and all data were collected for these seedlings.The results revealed that there was midday depression with evening recovery of effective photochemical efficiency of PSII (ΔF/Fm') and maximum photochemical efficiency of PSII (Fv/Fm) in all seedlings throughout the measurement course reflecting the capability of both provenances to keep intact photosynthetic apparatus for more than nineteen days under drying soil. Substantial direct correlation between ΔF/Fm' and electron transport for both provenances and inverse relationship between air temperature and Fv/Fm for P1 were established. Cyclic droughts affected negatively on the morphology of seedlings for both provenances as the height, stem diameter, and leaf number of water stressed seedlings was reduced substantially compared to well-watered. P1 seems to have greater morphological growth compared to P2 hence El Fasher's provenance tends to be more appropriate for plantations in arid environments.