In the mining basin of the Gafsa region in southwestern Tunisia, environmental exposure to randomly discharged phosphate-processing wastewaters (PPWW) presents a serious threat to health and the surrounding ecosystems. Thus, the contaminated areas are in continuous deterioration over time. There is a paucity of information on the deleterious effects of this kind of effluent. In the current work, the PPWW characterization showed the presence of high contents of Pb (0.90 ± 0.02 mg/L), Cd (0.35 ± 0.27 mg/L), Cr (0.43 ± 0.1 mg/L) and Fe (215.1 ± 2.41 mg/L), exceeding the permissible limits. To assess the chronic toxicity of the effluent in mammalians, two doses of PPWW (50% and 100%) were administered by gavage to Wistar rats for 28 consecutive days. The results revealed that the two PPWW concentrations significantly increased the plasma biochemical markers (bilirubin, alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and lactate dehydrogenase (LDH)), compared to untreated animals. Moreover, PPWW treatment severely altered the lipid profile by increasing the contents of triglycerides, total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-cholesterol) by 143%, 114%, and 91%, respectively, and significantly reduced the high-density lipoprotein cholesterol (HDL-cholesterol) level by 46%, compared to the control animals. In addition to the significant decrease in activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) in the liver of intoxicated rats, the malondialdehyde (MDA) level was remarkably altered. All of these were associated with deep histopathological damages, materialized by dilatation of sinusoids, congestion of the centrilobular vein, and inflammatory cell infiltration. These disturbances were accompanied by metal detection in the liver and blood. Additionally, DNA fragmentation detected in hepatic tissues highlighted the genotoxic effects of PPWW. All of the aforementioned effects occurred in a PPWW dose-dependent manner. These findings evidenced, for the first time, the in vivo-deleterious impacts of this type of effluent on mammalians inhabiting the mining basin area and therefore showed the real threats to which humans, as consumers, could be exposed. Accordingly, there is a dire need to pay special attention to PPWW before being discharged into environmental ecosystems without any prior treatments.