The abundance and preferences of individual invertebrate populations (including zooplankton) closely associated with the substrates provided by aquatic plant structures and open-water areas of Lake Nasser were quantified in this study in order to gain understanding of the importance of submerged macrophyte for invertebrate diversity, and their relation to water properties. The following water parameters were measured: temperature, pH, dissolved oxygen (DO), total dissolved salts, electrical conductivity, turbidity, total suspended solids, carbonate, bicarbonate, nitrate, nitrite, phosphate, sulphate, silica, potassium, total hardness, calcium and magnesium.Five macrophyte species were recorded: Myriopyllum spicatum, Najas horrida, Potamogeton schweinfurthii, Potamogeton pectinatus and Vallisneria spiralis. In total 67 invertebrate species were recorded, comprising 39 Rotifera, 12 Cladocera, 4 Copepoda, 4 Insecta, 2 Protozoa, 2 Ostracoda and one species of Turbellaria, Tardigrada, Annelida and Nematoda. Thirty-seven species were exclusively epiphytic, 11 species were collectively planktonic and 19 species were found in both habitats. The greatest abundance of epiphytic invertebrates occurred in association with N. horrida-P. schweinfurthii community.The results indicated that total suspended solids (TSS), TH and NO 2 are the most influential water variables on the distribution of the aquatic macrophyte samples and their invertebrate communities. Also, the study indicates that water variables have a higher impact on the aquatic macrophytes than on the associated invertebrate populations. P, NO 3 , K, Na, Mg, Cl and DO were the most influential water variables that dictate the distribution of invertebrate groups recorded in the open-water zone. Water temperature, electric conductivity, pH, NO 2 , SO 4 ÀÀ , SiO 3 À , CO 3 ÀÀ and turbidity have a lesser influence of the distribution of the invertebrates recorded in this zone.