The study concerns the Moulouya Estuary River, the second-longest African river that flows into the Mediterranean Sea, to evaluate the impact of wastewater discharges on water quality regarding its physicochemical and microbiological composition. The results showed that most studied parameters were influenced by seasonal variation and changed significantly from upstream to downstream (p < 0.05). The mean values of water temperature (22.5°C), pH (8.4), dissolved oxygen (6.7 mg/l), orthophosphate (0.03 mg/l), biological oxygen demand (5.9 mg/l), nitrates (10.12 mg/l), total suspended solids (89.75 mg/l), copper (7.8 µg/l), fecal streptococci (36 CFU/100 ml), fecal coliforms (81.5 CFU/100 ml), and total coliforms (179.5), conforms with the recommended surface water quality limits indicating excellent to good quality, except for, electrical conductivity (31618 µs/cm), sulfate (1049 mg/l), lead (116.67 µg/l), and cadmium (5.09 µg/l) indicating poor surface water quality. The mean values of Pb, Cu, and Cd exceed the limits values recommended for aquatic life. The water quality index (CCMEWQI) represents the overall quality, showing that the river studied is frequently threatened, and the conditions often deviate from desirable levels for aquatic life. The pollution index (PI) indicates that the water of Moulouya Estuary is slightly affected by Pb. However, the Metal Index (MI) indicates a significant environmental risk. Furthermore, a gradient of the Metal Pollution Index (MPI) was recorded in studied sites following the order: S2>S3>S4>S1. Although the study area does not present a significant microbial contamination problem, heavy metals and high-water mineralization are major concerns. These factors can have adverse effects on aquatic organisms and ecosystems, requiring attention and appropriate management measures to limit their impact.