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The study concerns the analysis of physicochemical and metallic parameters of the waters of the Moulouya River in order to establish a diagnosis of pollution degree of these waters and their possible impact on fish. Water samples were taken from six stations on the lower part of the Moulouya River and a station on the left bank tributary of the Oued Sebra, during the period from July 2017 to May 2018. The results obtained showed high levels of Electrical conductivity, Suspended Matter, Chemical Oxygen Demand, Biochemical Oxygen Demand, Ammonium, Nitrate, Sulfate and Chloride that exceeded the recommended limits for surface waters and fish water in many stations. In addition, the results showed a worrying situation of water quality of the station of Oued Sebra which receives industrial discharges and domestic waste. Furthermore, water analysis for trace metals showed relatively high levels but remains below the Moroccan standard for surface water and fish water. These results indicate that the waters of the Moulouya River can have adverse effects on the health and welfare of fish. Thus, the results of the Principal Component Analysis (PCA) showed an inter-station variability and corroborated the results of the descriptive analysis.