The effect of 3D printed modified Chitosan membranes on bacterial strains by water filtration system was explored in this study. Specifically, it focused on the characterisation of 3D printed Chitosan–graphene oxide–silver nanoparticles (CS–GO–AgNP) composite membranes and the effects of Dimethylacetamide (DMAc) used as co-solvent on the performance of the CS–GO–AgNP nanocomposites. It also examined the impact of GO–AgNP on the CS matrix for inhibition of Fecal Coliforms, Total Coliforms and Escherichia coli (E. coli) bacterial strains in contaminated surface water. The increase in DMAc concentration and subsequent reduction in CS mole fraction within the ink formulation resulted to wider distribution of AgNP across membrane surface, improvement in mechanical strength and surface hydrophilicity of the modified CS membranes. Similarly, increase in GO–AgNP concentration effectively reduced the spread of the identified microorganisms. Sample B-12 with 79% CS, 21% DMAc and 1.2 ml of GO–AgNP exhibited the highest inhibition of the bacterial strains, with more than 95% of Fecal and Total Coliforms suppressed or inactivated, while 99.9% of the E. coli bacterial cells were completely prevented, indicating that our 3D printed modified CS membranes can effectively be used for water treatment.