This research was initiated to assess and manage water quality status of fourteen surface drinking water intakes in El‐Beheira Governorate, Egypt. The study was conducted on four main branches of water resources in the governorate. Three water quality indices (WQIs) and two multivariate statistical techniques were applied, based on the Egyptian guidelines for the Nile River. Water quality records were collected for two successive years, 2014 and 2015, and were analyzed by descriptive statistics. The results revealed the critical water quality status of the four branches at the fourteen intakes. The multivariate statistical techniques returned the critical water quality conditions to the agricultural drainage and the domestic wastewater discharges. In addition, a new software application was developed to manage WQIs calculation. An urgent water quality monitoring and assessment system should be initiated for the drinking water resources all over Egypt, based on the developed water quality assessment techniques of this study. Practitioner points Three different WQIs and two different statistics tools were applied. Critical water quality status for the investigated surface drinking water intakes was reported. Agricultural drainage then domestic effluents are the main pollution sources. A new software application was developed to calculate WQIs to support decision makers.