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A constructed wetland (CW) in arid areas requires special knowledge given the particular climatic conditions. Among other aspects, the Hydraulic Retention Time (HRT) and plant species may be two important design parameters in hyper- and super-arid areas. Therefore, the study aimed to evaluate the influence of both variables in the application of CW in super-arid areas. Two HRT, 3.5 d and 7 d, and plant species classified by their origin: (a) native, Festuca Orthopylla, Cortaderia atacamensis and Schoenoplectus americanus, and (b) foreign, Cyperus papyrus, were evaluated in four Mesocosm Constructed Wetlands (MCW) operated in a super-arid area. The results showed that the HRT significantly increased ( < 0.05) in more than 10% the removal efficiency of nitrogen and phosphorus forms (TN, NH4+-N, TP, PO4-3-P). These results were the same for the two groups of plants assessed. Moreover, Cyperus papyrus significantly increased ( < 0.05) above 30% the removal efficiency, but only for nitrogen and phosphorus forms. MCW with this plant species showed a water loss above 25% and significantly increased ( < 0.05) the Electrical Conductivity (EC) of effluents. MCW planted with Schoenoplectus americanus showed water losses of around 25% for the both HRT evaluated, and its influence was not significant ( > 0.05) on the EC of the effluents. These results suggest that Schoenoplectus americanus would be an ideal candidate species for use in CW with subsurface flow in super-arid areas, with HRT varying between 3.5 d and 7 d.