In this study, four types of ceramic nanofiltration membranes, coded as M-SiO2, M-TiO2, LC1 and LC2, were investigated to comprehensively evaluate the influences of their characteristics on the removal of pharmaceutically active compounds (PhACs), as well as the anti-organic fouling performance and cleaning efficiency. Compared with some widely used polymeric NF membranes (e.g. NF90 and NF270), the ceramic NF membranes owned larger molecular weight cut-offs (MWCO), higher hydrophilicity, lower surface roughness and less negative charge. For PhACs removal, size exclusion was the primary mechanism, followed by electrostatic interaction. Hydrophobic interaction played a minor role for all of the ceramic membranes. The ceramic NF membranes demonstrated good anti-organic fouling properties. The membrane roughness and negatively charged (carboxylic and hydroxyl) group density together with membrane pore size determined the severity of overall fouling. Organic fouling on ceramic membranes had a relatively insignificant impact on PhAC rejection. Both water cleaning and NaOH cleaning could restore the water permeability to a high level compared to polymeric NF membranes. The smaller portions of irreversible fouling were mainly the results of much lower density of carboxylic groups on membrane surface.