The process of desalination through filtering membranes leads to the issue of generating a residue with a high concentration of salts, called concentrate. This residue is an environmental pollutant, especially when desalination is carried out far away from the sea (i.g., desalination in northeastern Brazil). In this context, the objective of the present research was to study the valorization of desalination concentrate through an aquaponic system. The feed water (brackish water) was desalinated, generating the concentrate, which was used for the operation of the experimental aquaponic pilot system in the cultivation of Litopenaeus vannamei (known as Pacific white shrimp) and New Zealand spinach (Tetragonia tetragonioides) in microbial biofloc. The initial average weight of the shrimp was 1.5 g and the stocking density used in the culture was 250 shrimp m−3. The experiment was carried out for 74 days, and the final weight was 14.57 g and survival was 18 %. The low survival may be due to the high concentration of nitrite in the culture water 11.75 mg/L, which can be toxic to shrimp, and also due to the ionic balance of the system that was not close to seawater. Therefore, it is recommended to start the experiment when the biofloco system is in the chemoautotrophic stage, with the nitrification process established, or work with higher salinity. The spinach experiment was carried out for 49 days, with an initial biomass of 29.38 g and a final biomass of 519.41 g. Iron deficit was observed in the spinach leaves, thus, adding iron into the system is recommended. The results obtained could encourage the use of technology that is simple to apply and brings benefits to the community. Thus, the valorization of the waste produced in the desalination of water by reverse osmosis membranes reduces its inherent impact on the deposition of concentrate in natural environments.