This study focuses on the physico-chemical characterization and organic pollution parameter of water, in six natural wetlands of the vast region of the northern Sahara: Lake Temacie, Lake Megarine and Oued Still, Oued Djedi, Lake Ayata, Oued Zemar (Biskra). The surveys conducted between October 2016 and Mais 2017, showed that the majority of sites are slightly turbid, brackish or salty with a low conductivity has strong depending on salinity, and a pH moderately alkaline. The concentrations of the studied ions (NH4+ and PO4-3) are high at Oued Djedi and Lake Ayata compared to the other sites, and for Nitrite (NO2-) are very high at Oued Djedi than that of the other sites. The organic pollution parameters are diverse from one site to another. The values of TSS (Suspended Solids) are higher for the current hydrosystem compared to the stagnant hydrosystem, the values of COD (Biological Oxygen Demand) are varied between (32 mg/l) and (85 mg/l), denotes an important organic pollution at the level of Lake Megarine and Oued Still and Oued Zemar (Biskra) which are much more subjected to anthropic action.