Surface water and groundwater pollution are important global issues affecting ecosystems and public health, especially in areas where untreated wastewater is reused for agriculture and domestic purposes. The Khoumane Wadi, a river crossing the Moulay Idriss Zerhoun region in northern Morocco, is an emblematic case study of this environmental problem. It is subject to persistent pollution, mainly due to discharges of untreated domestic wastewater. The reuse of this contaminated water for irrigating agriculture and domestic purposes has led to the subsequent pollution of the region’s groundwater resources. This situation causes serious health and environmental risks to locals and the ecosystem. The presence of biological, physico-chemical, and parasitological pollutants within the wadi becomes a major risk for substantial threat to groundwater quality and public health. The aim of this study is to assess the level of surface water pollution of Khoumane Wadi, and its contribution as a source of groundwater pollution in the Moulay Idriss Zerhoun region. The main objectives were to determine the level of pollution, its environment and public health effects and recommend effective mitigation strategies. The samples were collected and analyzed for a series of physical–chemical, bacteriological, and parasitological parameters. The results indicate that the Khoumane Wadi water is extremely polluted, and the levels of contaminants are higher than the environment and health standards. This pollution has a harmful effect on the quality of groundwater, which increases the risk of waterborne and parasitic diseases in addition to problems related to contaminated water consumption. The study serves to limit pollution and reveal the need for stringent measures to protect public health and the local ecosystem.