Organic micropollutants enter effluent streams and then flow into receiving waters. The volume adversely affects aquatic biota substantially. Therefore, many efforts have been made to develop methods for their elimination. The aim of this study was the removal of organic micropollutants with different properties from WWTP (wastewater treatment plant) effluent in fixed bed columns packed with several combinations of sand, granular activated carbon (GAC), and granular clay-carbonaceous composite. Two types of bentonite-powder activated carbon-based granules (Ben-AC) were prepared within this work, with different calcination temperature. It was found that higher calcination temperature enhanced the surface porosity and adsorption potential versus studied micropollutants due to dihydroxylation resulting in higher chemical activity. Introduction of these granules in the place of GAC in a fixed bed column enhances the removal degree of micropollutants and typical water quality parameters. For example, the reduction degree of color, phosphate, and nitrate concentrations increased from 83%, 69%, and 4% to 95%, 83%, and 24% for column I and II, respectively. The concentration of carbamazepine, octylphenol, nononylphenol, and anthracene was reduced by 75%, 83%, 72%, 99% in column I, while using column II or III their removal was: 86%, 97%, 99%, 99%, respectively. Independent of the column filling, the removal of carbamazepine was the lowest (75–86%), while the highest retention was obtained for anthracene (99%). The study of column performance in the treatment of effluent in time showed that column filled with Ben-AC-400 guaranteed high removal degree in the operating time. The batch adsorption data were better described by both the Langmuir model.