This paper presents the first results of 1-year survey of aquatic Diptera, carried out in two Moroccan High Atlas rivers, Assif Ahançal and Assif n’Aït Bouguemaz, which are registered as Ramsar sites and drain a large part of the mountainous Geopark of Mgoun. This survey, which consists in a first study of the longitudinal distribution of these insects, occurs during the period September 2019–July 2020, at high and medium altitudes (1086–2408 m). Limited to immature stages, this study permitted to collect 561 specimens of Diptera from 16 river sections, mainly using a Surber-net sampler. Among the collected material, we were able to identify 38 genera and 11 species, belonging to five families. This fauna is relatively rich in new taxa for Morocco or for the High Atlas mountains. Indeed, two Chironomidae species, Macropelopia notata (Meigen, 1818) and Psectrocladius (Allopsectrocladius) flavus (Johannsen, 1905), and one Tipulidae, Tipula (Yamatotipula) pierrei, Tonnoir, 1921, are newly recorded in Morocco, as well as five genera: three Chironomidae (Krenopelopia, Fittkau; Natarsia, Fittkau; and Psilometriocnemus, Saether), one Empididae (Chelifera, Macquart), and one Ceratopogonidae (Atrichopogon, Kieffer). Two other species, Parachironomus frequens (Johannsen) and Heterotrissocladius marcidus (Walker), and seven genera are reported as new taxa in the High Atlas. The two rivers have similar richness (21 taxa each), mainly due to Chironomidae (94%), the most abundant and diversified family. The Empididae (4.8%) are relatively under-represented in the two rivers, as well as the other families (Ceratopogonidae, Tipulidae, and Tabanidae), which do not exceed 1% of the total dipteran abundance. The vertical distribution of the taxa revealed significant influence of the altitude on community compositions and distributions. In waiting to collect adults, immature dipteran stages prove the high abundance and diversity of the benthic entomological assemblages, which give hope that a more deep study of the dipteran fauna in the two Ramsar sites will provide remarkable novelties, in both systematic and ecological domains. It is also expected that this study will permit to assess the aquatic biodiversity of these ecosystems and its sensitivity to the increasing human disturbances.