Groundwater has many characteristics that make it preferable as water supply. But once becomes contaminated, its location and low rate of replacement with fresh water makes it difficult to return it to its pristine state. Toxic and organic chemical pollutants pose threat to the safety of water resources in Khartoum. Contamination of the river Nile system leads to contamination of groundwater resources.Present study aimed to evaluate the current chemical quality of Khartoum state groundwater resources in terms of its heavy metals and refractory organic content. A comparison of the obtained result with national and international standards was also carried out.To realize the objective of this study, a quantitative analysis of nine samples collected from three boreholes named A (Dar Alsalam block (21) ), B (Alkaadarow Almadaris) and C (Alazhari block (15)) during three seasons; autumn, winter and summer were investigated. Heavy metals concentrations (Pb, Cr, Cd and Fe) were determined using Inductively Coupled Plasma- Atomic Emission Spectrometer (ICP- AES). For refractory organic compounds, TOC and BOD5 tests were carried out, the ultimate value (BODu) was calculated as 1.7 BOD5 and then the difference between TOC and BODu was estimated as the concentration of refractory organic compounds.The result showed that groundwater boreholes were safe with respect to cadmium, iron and chromium pollutants, but they contain high levels of lead and refractory organic compounds. The concentrations of lead exceeded both national and international permissible levels which are expected to be due to infiltration of poorly treated sewage and some industrial effluents or from the process of recharging groundwater by contaminated surface water. Since there are no treatment processes in water supply treatment plants targeting the removal of these pollutants, populations consuming this water are expected to be exposed to many health hazards.