A tertiary treatment of the effluent received from five Tunisian wastewater treatment plants is implemented at GDA Sidi Amor for reuse in an aquaponic system. It includes a MBBR, a constructed wetland, sand and activated carbon filters, and a combined nanofiltration and reverse osmosis desalination system. The Results show that the post-treatment before desalination reduces the COD by 44 % which is mostly refractory, the orthophosphate by 33 %, and the ammonia by 95.6 %. The NF90 4040 removes 2/3 of the salts and micropollutants except for sodium, chloride and nitrate which are respectively 57 %, 45 %, 39 %. The micropollutants benzotriazole, and clarithromycin were removed by 17 %, and 8 % respectively. The optimum pressure for a conversion rate of around 80 % is 4.7 bar for the cold period and 7 bar for the summer period depending on water salinity and membrane fouling. After one year, membrane permeability decreases. After cleaning the conversion rate increases to 89 % at 5.2 bars and the hydraulic permeability increases by 39 %. Using the hybrid system NF-RO at 10 bars for RO BW30–4040 the amount of brine was reduced by 65 % and the permeate quality is improved. After five months, the total fish weight increases by 21 kg and the crops grow well.