Groundwater is an important water resource in the Helwan area, not only for drinking and agricultural purposes, but also because several famous mineral springs have their origin in the fractured carbonate aquifer of the region. The area is heavily populated with a high density of industrial activities which may pose a risk for groundwater and surface water resources. The groundwater and surface water quality was investigated as a basis for more future investigations. The results revealed highly variable water hydrochemistry. High values of chloride, sulphate, hardness and significant mineralization were detected under the industrial and high-density urban areas. High nitrate contents in the groundwater recorded in the southern part of the study area are probably due to irrigation and sewage infiltrations from the sewage treatment station. The presence of shale and marl intercalation within the fissured and cavernous limestone aquifer promotes the exchange reactions and dissolution processes. The groundwater type is sodium, sulphate, chloride reflecting more mineralized than surface water. The results also showed that water in the study area (except the Nile water) is unsuitable for drinking purposes, but it can be used for irrigation and industrial purposes with some restrictions.