The effect of water pollution used for irrigation on the distribution of the weeds associated with the cultivated crops were studied in nine sites along Bahr El Baqar drain. The field survey revealed the presence of 63 species belonging to 22 families along the studied sites. The most dominant families were Poaceae, followed by Asteraceae, Amaranthaceae and Cyperaceae; while Euphorbiaceae, Tamaricaceae and Apiaceae were the lowest-represented families. Canonical Correspondence Analysis (CCA) of the soil chemical constituents showed that sodium, electrical conductivity (EC), sulphates and chloride were the most effective soil variables controlling the weed distribution along Bahr El Baqar drain in studied nine sites. Data showed that salinity indicator species as Spergularia marina (L.) Besser, Cressa cretica L. and Imperata cylindrica (L.) Raeusch. were common at high salinity and EC; while waste land indicator species such as Arundo donax L., Dysphania ambrosioides (L.) Mosyakin & Clemants and Chenopodium murale L. were also documented. This work includes the taxonomic studies of the species distributed along Bahr El Baqar drain, including the species identification and updates classification. Finally, this study highlights the negative effect of the polluted water used for irrigation on soil and crop-associated weeds.