For the first time, comprehensive phycological screening on El-Farafra Oasis (Western Desert, Egypt) had been implemented for unveiling and characterization of its cryptic algal diversification, with special interest on springs and drilled wells. Overall during summer 2011 and winter 2012, 82 different algal taxa have been found in all studied habitats as naturally-grown and culture-induced propagations. Of these, different 14 algal strains have been recorded only using water-culturing techniques on different four algal media (Kolkwitz's solution, Chu #10, BBM and modified BG-11 media). Culturing techniques not only permitted to discover the cryptic algal taxa present in the viable spores state, but also allowed to follow and confirm the complete life cycle of the rare stigonematalean true T-branched cyanoprokaryote Westiellopsis prolifica. This inventory enriched the freshwater Egyptian algal flora with 6 new algal taxa for the first time namely Symploca dubia, Westiellopsis prolifica, Euastrum insulare, Penium margaritaceum, Zygnemopsis sp. and Nitellopsis obtusa. In this study, some recorded taxa are considered to be crenophilous, e.g. Geitlerinema jasorvense and Phormidium carboniciphilum, to be crenoxenic e.g. Jaaginema subtilissimum, Phormidium corium, Westiellopsis prolifica and Zygnemopsis sp. Only, Oscillatoria tenuis had the highest-grade constancy of occurrence throughout the whole investigation period. This species shows a strong α-mesosaprobic indication for water eutrophication in this oasis. In general, El-Farafra Oasis wells and springs are considered isolated and "azonal" habitats still bearing partially near-natural conditions with some agricultural, pastures and humans impacts, and have freshwater type with slight seasonal variations in their mineralization contents as a kind of ecotones-characteristic features. Finally, these hyper-arid-desert-dwelling water systems are just about excellent potable water resources in the context of water quality guidelines of Egyptian Higher Committee for Water (EHCW) and World Health Organization (WHO), but they substantially still need special governmental efforts in the future to mainly eliminate the relatively high contents of Fe, Mn and Zn.