Nile River is the main source of fresh water for domestic, agriculture, industry, fisheries and tourism purposes for most governorates in Egypt. Unfortunately, most of the drinking water plant intakes on Nile River. It is impacted by increasing concentrations of pollutants resulted from the agricultural drains located along its sides, industrial effluents and domestic waste from villages which have no sanitation system.  This study aims at monitoring total coliform, Escherichia coli (E.coli), algae which may be related with the risk of diarrheal diseases and other diseases if they are present in water and suggesting limits for them in the criteria of drinking water plant intakes at Article 49 from decree No. 92 of 2013 in law No. 48 of 1982 for the protection of Nile River from pollution . Samples from the drinking water plants intakes were collected in four seasons from September 2016 to October 2017. Each source of water samples was collected every month at three governorates : Cairo from (Al amarya - Al Tepeen - Manial Al Rawdah - Maadi ), Giza from (Embaba - El Saff - Gazirat Al Dahab -Giza - Al Hawamdiyah - Kafr Kandeel ), and Kalyobia from (Abo Zaabal - Al Reeyah El Tawfekey - El-Abadla - Basoos - Qualube ) . The total numbers of samples were collected 210 to investigate: Total Coliform, Escherichia coli and algal count. Results showed that the Nile water at the studied locations contains high count of pathogenic indicator bacteria and algae where the mean of most probable number is 29859 /100ml, 5923 /100ml and 2656 unit / 1ml for total coliform, Escherichia coli and algal count respectively. Diatoms is the prevalent algae type with percent 73.3% followed by green algae with percent 24 %and the lowest is Cyanobacteria (blue green) with percent 2.7 %. Chemical oxygen demand (COD) was not complying with law No. 48 of 1982 in six intakes.