Pollution in freshwater canals is given a great interest due to its bad impacts on humans, animals and fish wealth. The objective of this research is to formulate a methodology to help water planner and water resources engineers for sufficient use of water to avoid harmful impacts from polluted water in Sharkia Governorate in East Nile Delta. Therefore, 59 water samples were collected from different locations along with the canals network. Canals water quality variation is detected using a weighted spatial overlay method inside geographic information system software (GIS). Accordingly, the weighted spatial water quality model (WSWQM) was performed inside the GIS system to determine spatial variation in water quality of the studied canals. Ten effective water quality parameters for the collected water samples were used as thematic layers to build the WSWQM model. These parameters include; total dissolved solids, pH, water hardness, dissolved oxygen, biological oxygen demand, chemical oxygen demand, nitrate, fluoride, ammonium, and fecal colon bacteria. The WSWQM was run and a water quality map was resulted and classified the studied canals into five classes ranging from very low to very high-water quality. High and very high-water quality classes are observed in the southern parts of the study area, whereas the low and very low classes are represented by the northern parts of the study area at ends of the studied canals. The obtained results may assist in providing a detailed overview of the polluted reaches of the studied canals, which help in the management process for this important water source.