The Loa River is the longest Chilean river with 440 km, located in the Atacama Desert. It has three tributaries’ rivers, and its fauna has been poorly studied, due to mainly access difficulties. The aim of the present study was the first characterization of benthic invertebrate community structure in a confluence of Loa and Salado rivers considering the derive invertebrates and benthic communities. The results revealed that species composition in benthic samples has no significant differences between Salado and Loa rivers before the confluence with Salado River, but both sites had significantly high species numbers in comparison to Loa River in Calama after Salado confluence whereass in derive species composition did not have species differences. Finally, the results of null models revealed that species number for three sites had no structured pattern for benthic and derive samples. Ecological and biogeographical topics were discussed here.