The present study aimed to characterize wastewater fractions obtained after the wet extraction of proteins from legumes. In addition, the suitability of wastewater fractions for the potential recovery of high value-added compounds was also examined, and consequently, the prevention of the environmental impact of these wastes was explored. Similar to the industrial production of proteins, wet alkaline and acidic extractions of proteins from faba bean and pea flours were performed in two stages of extraction. The different wastewater fractions were characterized by measuring their organic matter content, total solids (TS), total dissolved solids (TDS), electrical conductivity (EC), pH, and turbidity. The value-added compounds from these wastewater fractions were quantified, which included the protein content, carbohydrate content, phenolic content, and antioxidant activity. In addition, the phenolic compounds in these factions were identified and quantified. It was observed that the fractions obtained in the first extraction stage had 60%–90% higher organic matter content, measured as the chemical oxygen demand (COD), compared to the second fractions, indicating a higher environmental impact of the former in case of disposal. The results obtained for COD, TS, TDS, EC, pH, and turbidity demonstrated that microfiltration reduced only the turbidity (85%), and consequently, a decrease was observed in the particulate matter, while there was a practically negligible reduction in the soluble matter. Wastewater from faba exhibited the highest polyphenol content and antioxidant activity, and was, therefore, considered the most valuable fraction for potential valorization.