Pressure-based membrane processes represent excellent water resource recovery prospects from industrial waste streams. In contrast with conventional pretreatment technologies, studies have shown that membrane pretreatment applications, such as microfiltration (MF), are more cost-effective and improve the results of the overall treatment processes. Hence, enhancing rejection efficiency of MF will enhance the performance of any downstream treatment processes. In this study, 0.45 µm cellulose acetate (CA) microfiltration membranes were modified by vacuum filtration-assisted layer-by-layer deposition of bilayers composed of negatively charged graphene oxide (GO) and positively charged polyethyleneimine (PEI). The performance of 1-, 2-, and 4-bilayer GO–PEI-modified membranes were investigated for their dye-rejection of anionic eriochrome black T (EBT) dye and cationic methylene blue (MB) dye in a cross-flow membrane module. As the number of bilayers on the membrane increased, the membrane thicknesses increased, and the deionized (DI) water flux through the membranes decreased from 4877 LMH/bar for the control (no bilayer) membrane to 2890 LMH/bar for the 4-bilayer membrane. Conversely, the dye-rejection performance of the modified membranes increased as increasing bilayers of GO–PEI deposited on the membranes. The anionic EBT dye saw superior rejection (~90% rejection) compared to the cationic MB dye (~80% rejection), which can be attributable to the electrostatic repulsion between the negatively charged GO surface and anionic EBT dye. After 50% recovery of the saline and dye-laden feed water, there was an observed drop in DI water fluxes of ~40–41% and 36%, respectively. There was also a slight increase in EBT dye-rejection during the composite feed-water experiments, attributed to the precipitation of salts on the membrane feed side or pore spaces, which subsequently reduce the membrane pore sizes.