Abstract: Aquatic biodiversity is one of the most essential characteristics of the aquatic ecosystem for maintaining its stability and a means of coping with any environmental change. South Sinai is one of the most ecologically important regions in Egypt. The location of the peninsula of Sinai makes it one of the most characteristic of the Egyptian faunistic regions and it contains very different geomorphological units. It lies at the confluence of three zoogeographic regions (Afrotropical, Palaearctic and Oriental), which makes its fauna and flora special. Twenty nine species, in 24 genera, belonging to 16 families were collected. Species richness, species evenness, Simpson diversity index, Shannon diversity index and species composition were assessed using different statistical methods. There is a high significant difference obtained in aquatic insect’s diversity and their richness between the two studied localities. Habitat heterogeneity within a locality may also affect aquatic insects’ diversity. The diversity of aquatic insects between natural and artificial pools showed a significant difference in the Simpson diversity index as it was 0.889 for natural pools and was 0.701 in the artificial pools. Also, there is a significant difference in the Shannon diversity index, as it was 2.418 for natural pools and was 1.6 in the artificial pools. Similarity among drainage systems graphed by DCA (detrended correspondences analysis) and cluster analysis showed discrimination of three drainage systems within the locality of Saint Katherine from the remaining two drainage systems within wadi Feiran. Moreover, the Jaccard’s similarity index was measured among different localities in the study area.