During the period of February 2004 to April 2005, 74 samples from various forms of algal vegetations were collected from different periphytic freshwater habitats in Sultanate of Oman. These habitats include water streams of Aflaj systems, springs, wadis and rocky mountain regions of El-Dakhilia, Al-Dhahirah, Al-Batinah, Al-Sharquyah, and Muscat. Thirty cyanobacterial taxa were identified based on their morphological characteristics. Distribution analysis of the cyanobacterial flora in correlation with the studied areas obviously emphasized that the locality of Al-Taeen was the richest site, while localities of Bahla, Al-Hamra, Wadi Al-Moudin, Wadi Tanouf in Nazwa were the poorest sites by the diversified cyanobacterial flora. The microscopic identification of the natural assemblages of the biotopes of the studied localities indicated the presence of seventeen taxa of chlorophytes. The autecology of green algae revealed that the appearance and existence of rhizobenthic Chara canescens and the unbranched filaments of Rhizoclonium heiroglyphieum strongly confirmed the hardness of water habitats of Jalan area in Al-Sharquyah. On the other hand, water habitats of Nazwa area were found to be the suitable environments favoring the growth and dominancy of freshwater periphytic chlorophytes. Fifteen diatom taxa were identified from the investigated localities. The autecology of the identified diatom taxa of oligohalobien type (indicators for freshwater habitats), except Biddulphia laevis and Achnanthes brevipes var. intermedia of mesohalobien type of salinity. This observation added strength conformity for the hardness of water of Jalan locality.