Variations in macro-morphology, cyanobacterial community and nitrogen fixation of fully submerged cyanobacterial mats were studied in six ponds distributed along Wadi Al Khoud in Sultante of Oman. Cyanobacterial mats (CBM), complex assemblages of cyanobacteria, bacteria and algae, are important ecosystems, which are known to play a role in nitrogen cycle. These mats were rarely investigated in Wadis ecosystem, especially in the Arabian Gulf countries. The studied ponds exhibited similar chemical and physical properties except flow rates and underlying bottom. These exceptions were suggested to play a role in changing the macroscopic features of the mats. The mats showed variation in morphology and adherence surfaces, but were rich in cyanobacterial species. Three orders of cyanobacteria inhabited theses mats; Oscillatoria, Nostocales and Chroococcales, with Phormidium sp. and Calothrix sp. as the most dominant cyanobacteria. The latter, performed nitrogen fixation via terminal heterocyst at a rate of 51.872 nmol ethylene ml" do measured by acetylene reduction assay (ARA). Most nitrogen fixation in mats was carried out by cyanobacteria in light at a rate of 254.19 nmol ethylene cm" d"?. The nitrogenase activity of a single cyanobacterial mat was not affected by spatial distribution along one particular pond (in-welling to out-welling). 15 dominant taxa of macroinvertebrates were abundantly found in the Wadi with, Mayflies insects as the dominant taxa. Effect of flooding on both acetylene reduction rates and phototrophs abundance in cyanobacterial mats were investigated. Flooding caused flushing out of old mats and new mats reestablished over surfaces of rocks. Some of these mats had significantly higher rates of ARA than those existed prior flood. After flood, higher growth of epilthic algae at the surface of the ponds and a fluctuation in the abundance of benthic phototrophs (Chl a) were recorded. These changes could be a result of the availability of nutrients in the water column as well as the effect of grazers.