Purpose The purpose of this paper is to assess the water quality parameters resulting on: First, the flow direction in biofilters (ascending or descending), second, constructed wetland (CW) with local plant species and third, the combined system for the removal of organic matter and nutrients pollutants from water in arid regions. Design/methodology/approach An integrated system is presented and tested in situ with a vertical up-flow and down-flow biofilters. Two configurations schemes are followed by a three separated horizontal subsurface CWs: two planted with Phragmites australis, Typha latifolia and the third unplanted. The methodology is based on a statistical analysis of the collected data. Findings The present experiment demonstrated that the wetlands planted with P. australis and T. latifolia showed the highest removal. Moreover, T. latifolia performed better than P. australis for most of the parameters, notably in the first system, whereas the wetland efficiency indicated that P. australis contributed greatly to the removal of TP in the first system and NO3-N in the second system. In general, for the highest removal efficiencies of the combined biofilters and wetlands system, the present study demonstrated that the first system performed better than the second for all the parameters. Originality/value The originality of the research is that it compares in situ two biofilter systems: vertical up-flow and down-flow biofilters. To avoid the effects of domestic wastewater that is discharged directly without treatment in the Oued Righ channel or in the lake, this integrated system can be one of the alternatives for wastewater treatment, as it reveals the need to protect aquatic ecosystems in arid regions, and can decrease the risks to human health and the environment.