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Contamination with heavy metals is one of the most serious problems in the aquatic environments. In Egypt, Manzala Lake is suffering from this problem. The objective of this work was to assess heavy metals pollutants and their spatial distribution in Manzala Lake using GIS technique. Georeferenced water and sediment samples were randomly collected from the lake. The detected heavy metals were: Fe, Pb, Cu, Cd, Cr, Zn and Co. The obtained results indicated that the highest concentrations of heavy metals were observed in the northeastern and the southern parts of the lake nearby drains. This could be attributed to industrial, agricultural and municipal wastes coming through the drains especially Bahr El-Baqar drain and the industrial wastes coming from Port Said drains. From the geo-accumulation index, it was noticed that the lake is more polluted with cadmium and lead in the hydrosoils samples. All metals in water are within the EPA standard limit except for cadmium. Geostatistics provides effective methods to quantify the contaminated waters and sediments which support decision-making about redevelopment scenarios or remediation techniques.