The River Nile is the main source of water for agricultural, industrial, and municipal purposes in Egypt. A large number of canals transfer river water; there are separate drains for transporting agricultural (and at times sewage) run-off. Lake Qarun is a closed basin with a high evaporation rate. The only source of water in the lake is the agricultural and municipal drainage from the surrounding communities. The drainage waters are high in solids, nutrients, pesticides, heavy metals and organics. Little information is available on the water quality of Lake Qarun, and its fisheries resources. The objective of this research was to study the water quality characteristics of Lake Qarun and compare these with the quality of water in the River Nile and its canals. Lake Qarun's surface water -3 Km south of National Institute of Oceanography and Fisheries -is alkaline (pH 8.4), with high conductivity (95 mS/m) and a high total dissolved solids (TDS, 2.8 g/L), chloride (Cl, 164 ppm)), and ammonium-N (9.2 ppm). The dissolved oxygen (DO) content at a depth of 3 m is 3.5 ppm. Compared to River Nile and its canals, the water quality of Lake Qarun has significantly deteriorated from the large input of agricultural and domestic wastewaters.