Freshwater salinization increasingly threatens river ecosystems in arid regions. In situ studies on effects of salinity on freshwater communities are still scarce, especially in largely understudied areas of Africa. To compare macroinvertebrate communities in differing salinity levels, we conducted a confluence-based study in the Draa River basin in Morocco by focusing on two tributaries and their joint downstream sections, in the immediate vicinity of three confluences. Our study revealed that α-diversity differed only minimal. Although only around five taxa comprised over 90% of specimens per section, the more saline sections exhibited proportionally more salt-tolerant generalist species. There was lower β-diversity between the downstream section and each tributary compared to between tributaries, indicating a mixed community after the confluence. The trait profile of the saline El Mellah displayed more resistance and resilience traits to disturbances than the less saline Iriri. Furthermore, low water flow reduced the abundance of sensitive taxa. Overall, we observed minimal differences in macroinvertebrate community composition, due to low γ-diversity in the basin. However, the confluence-based study design remains valuable for investigating effects of specific stressors on ecosystems by excluding large-scale geographic patterns, as compared sites are close and therefore share the same climate, geology, and altitude.