Desalinated brackish water is becoming an important water source for agricultural irrigation. In Brackish water desalination, pretreatment of reverse osmosis is the key step in designing the plants to avoid membrane fouling and scaling. It is enormously important to carry out a study designed at ensuring the optimization of the pretreatment system for brackish desalination plant in order to optimize the quality of the water fed through the reverse osmosis membranes, to guarantee the highest performance and to minimize the number of shutdowns for chemical cleaning. In this paper, performance evaluation carried out for a brackish water reverse osmosis plant for agricultural application, located in Dokkala Region in Morocco. This plant showed poor performances after few months of operating and frequent shutdown. The operating pressure increased significantly and the permeate conductivity decreased surprisingly. To identify the causes for the poor performance, different investigations were carried out. Thus, the pretreatment scheme was thoroughly reviewed to find out the causes of anomalies. The problem was resolved by removing chlorination and sodium bisulfate steps from the pretreatment.