Sixteen stations were sampled (four successive seasons) during 2011. Physical and chemical characters of water in combination with surface sediment were sampled from Isamilia Canal and its branches. Diatoms dominated the epipelon community, whereas chlorophytes and cyanobacteria were rarely present. One hundred sixty-seven epipelic species were recorded. Diatoms were dominated by the centric diatoms Cyclotella spp. and Aulecosiera spp. Most frequent diatom species underwent multivariate analysis of TWINSAPN to clarify the classification of diatom species and CCA to correlate diatom species to the most effective environmental parameters. Most species were positively affected by eutrophication, PO₄ and NH₃, and seasonal related factor, temperature, whereas they were negatively affected by pH and SiO₂. The applicability of Trophic Diatoms Index (TDI) was tested in the area of study. The results of the TDI revealed that the majority of the canal stations were in the acceptable ring but showed non-significant relation with the eutrophication parameters. The application of diatoms based indices developed in foreign countries cannot be applicable in egyptian environment and the development of indices based on the egyptian ecoregions is very obligatory.