In this research, ceramic nanofiltration (NF) membranes were prepared by depositing alumina-zirconia (Al-Zr) nanoparticles into the pores of ceramic ultrafiltration (UF) membranes for the removal of radioactive uranium in an aquatic system. The modified ceramic membranes showed NF membrane performance with around 1,000 Da molecular weight cut-off (MWCO) and 58% CaCl2 rejection. The removal efficiencies of uranium species by these successfully modified ceramic NF membranes exhibited differences depending on the pH conditions (pH 5.0, 7.4, and 10.0), and achieved the highest rejection of 91% at pH 7.4. This behavior is due to the dominant aqueous species of uranium in pH 7.4, (UO2)2CO3(OH3)−, which has the largest molecular weight among the conditions and the negatively charged species having electrostatic attraction to the positively charged ceramic NF membranes. The ceramic NF membrane prepared here is expected to be feasible in the advanced water treatment process to remove radioactive compounds.