The present work was conducted to document the problems raised regarding low-flow in the Rosetta branch, Egypt and to develop management options to protect drinking water sources. The water quality was monitored during low-flow periods at four drinking water intakes. Results showed an increase in electric conductivity (EC), ammonium (NH4), nitrite (NO2), phosphate (PO4), and total organic carbon (TOC) during the low-flow period. EC ranges from 454 to 1,062 μS/cm and the mean value is 744. Ammonium ranges from 0.38 to 18.5 mg/L and the mean value is 5.45. NO2, PO4, and TOC have mean values of 0.73, 1.85, and 6.71 mg/L, respectively. Statistical evaluation revealed the association of NH4, EC, and PO4 that are good indicators for the load of wastewater. High ammonium often refers to a bad situation regarding oxygen while high nitrite indicates the first oxidation for wastewater through microbiological processes. The low-flow action has a serious impact on drinking water source. A high content of ammonium has delayed coagulation, enhanced algae growth, and prevented the breakpoint being reached during chlorination processes. Potential management options to deal with water scarcity and low-flow, meanwhile reducing the contaminant load in the source drinking water were proposed.