Variations in distribution, species composition, and chemical constituents of aquatic macrophytes of Al-Rayah El Tawfiky (T) and Al-Rayah El Monoufy (M) in addition to their relations with bacterial communities structure and water variables were studied over the period from spring 2014 to winter 2015. Ten of the aquatic macrophytes species related to 7 families and 9 genera were recorded. Myriophyllum spicatum was the most dominant species, the autumn season and Al-Rayah (M) were the richest in species numbers. Protein, lipid, nitrogen, phosphorus, and potassium were detected at higher concentrations in Ceratophyllum demersum from Al-Rayah (T), however organic matter and nitrogen-free extracts contents attended their highest values in Potamogeton nodosus from Al-Rayah (M). Microbial analyses indicated the presence of total bacterial counts and the total diazotrophs in high population densities (Up to 10⁵). However, total and fecal coliforms populations are exceeding the permissible limits cited by World Health Organization, recorded their highest numbers in spring at the site of Al Rayah (M) which was occupied by Potamogeton nodose and Myriophyllum spicatum. A significant difference in chemical composition, distribution pattern, the community structure of aquatic macrophytes, and bacteria attributed to the seasons and site differences, in addition to the nutritional potential of the analyzed macrophytes species especially submerged ones were recorded.