Cellulosic nanomaterials are potential candidates in different areas, especially in water treatment. In the current work, palm fruit stalks cellulose nanofibers (CNF), TEMPO-oxidized CNF (OCNF), and activated carbon (AC) were used to make thin film membranes for removal of E. coli bacteria from water. Two types of layered membranes were produced: a single layer setup of crosslinked CNF and a two-layer setup of AC/OCNF (bottom) and crosslinked CNF (up) on hardened filter paper. The prepared membranes were evaluated regarding their microstructure and layers thickness using scanning electron microscopy (SEM). Water flux and rejection of E. coli bacteria was tested using dead end stirred cells at 1 MPa pressure. Thickness of the cosslinked CNF layer in both types of membranes was about 0.75 micron. The results showed that exchanging water by isopropyl alcohol before drying increased porosity of membranes, and thus resulted in increasing pure water flux and flux of bacteria suspension. The two-layer AC/OCNF/CNF membrane had much higher water flux than the single layer CNF due to higher porosity seen on the surface of the former. Both types of membranes showed high capability of removing E. coli bacteria (rejection ~96–99%) with slightly higher efficiency for the AC/OCNF/CNF membrane than CNF membrane. AC/OCNF/CNF membrane also showed resistance against growth of E. coli and S. aureus bacteria on the upper CNF surface while the single layer CNF membrane did not show resistance against growth of the aforementioned bacteria