The wastewater treatment involves various techniques at different technological levels. Treatment takes place in several stages, of which coagulation and flocculation are the most important. Most suspended solids are indeed eliminated during this stage by the addition of a coagulant. In this research, bio-coagulant was extracted from pumpkin seed (PS) waste after extraction of the essential oils, and used with ferric chloride to treat wastewater from the plant of Chalghoum El Aid-Oued El Athmania Mila. In this study, the Box–Behnken design (BBD) with three factors was used to investigate the effect of pH, organic coagulant dosage Pumpkin seed extract (PSE), and chemical coagulant dosage (FeCl₃) on coagulation–flocculation performance in relation to turbidity, chemical oxygen demand (COD), aromatic organic matter (UV 254), and phosphate. The main characteristics of the raw water were turbidity (250 NTU), COD (640 mg/L), UV 254 (0.893 cm⁻¹), and phosphate (0.115 mg/L). The results obtained were very significant. All the statistical estimators (R² ≥ 97% and p ≤ 0.05) reveal that the models developed are statistically validated for simulating the coagulation–flocculation process. It should be noted that the residual values of turbidity, COD, UV 254, and phosphate after treatment by this process were 0.754 NTU; 190.88 mg/L; 0.0028 cm⁻¹; and 0.0149 mg/L, respectively. In this case, the pH, bio-coagulant dosage, and chemical coagulant dosage values were 4; 17.81 mL/L; and 10 mL/L, respectively. In this study, Fourier-transform infrared spectrometer (FTIR) and scanning electron microscope (SEM) characterization of the bio-coagulant proved the presence of the active functional groups responsible for coagulation, namely carboxyl group.