The existence of water lately is quite alarming, especially in urban areas. The increasing of river water pollution through industrial and domestic waste, herbicide / pesticide and also the contaminant left-over cause the quality of river water getting worse beyond the allowance limit of standard for clean and drinking water. The most important criteria in examining clean and drinking is the ingredient test of microbiology with Escherichia Coli (E. Coli) bacteria, which is a patogenic bacteria to human, as the indicator. This study aims to remove E.Coli bacteria in water river in Geudong, Lhokseumawe using membrane filter made of ceramic mixturing with clay and fly ash n various compositions; clay:fly ash (40%:60%), clay:fly ash (50%:50%) and clay:fly ash (60%:40%). The ceramic membrane was made with sintering method in 700°C temperature for 4 hours and the filtration test was done in varios of operating pressure; 0,25; 0,50; 0,75, 1,00 and 1,25 bar. The result of the study showed that ceramic membrane with the composition of clay:fly ash (40%:60%) was able to reject E-Coli up to 99,048% with operating pressure 0,25 bar. Using Scanning Electron Microscopy (SEM) test, it is known that the ceramic membrane with the composition of clay-fly ash (40%:60%) is included as microfiltration membrane with pore size 1,6 μm – 2 μm.