The concentrations of some heavy metals in water of Bardawil Lagoon located in East northern Egypt, in relation with some abiotic variables were investigated in this study. The water quality characteristics over the sampling period and the levels of heavy metals from the Lagoon were evaluated from twelve stations covering the whole lagoon area through twelve successive cruises that commenced in January 2004 and ended in December 2004. The Lagoon water quality characteristics were mostly in the normal range for marine habitat and lied under the international permissible levels. The recorded levels of major cations and anions in the water lagoon were higher than the corresponding sea water levels and indicate its higher salinity level than sea water. In addition, the average values of nutrient salts and studied heavy metals (Fe, Mn, Zn, Cu and Pb) in the water samples were lorwer than the respective reference values for water. Based on this study, the human health risk for heavy metals in Bardawil Lagoon are still low at present.