The removal efficiency of 6 micro-grain AC (μGAC) was examined for 23 selected pharmaceutical compounds, usually found at trace level in municipal wastewater treatment plant (WWTP) effluents. Two different sets of experiments were carried out using distilled water and a real WWTP secondary effluent in order to understand the adsorption mechanisms of pharmaceuticals, including the role of the presence of background organic matter. Physical and chemical properties of μGACs and target pollutants were checked for their potential to predict the pharmaceutical removal. Textural properties of μGACs, and especially the mesopore volume, seemed to play the most important role during the adsorption without background organic matter whereas the chemistry of the μGACs, such as the presence of surface oxygen groups and the point of zero charge, could have more influence in the experiments with WWTP effluent water. Positively charged molecules are better adsorbed due to the influence of the background organic matter and the presence of oxygenated groups in the surface of the μGACs. The UV254 removal correlated well with the pharmaceutical removal and it is confirmed as an indicator to control the performance of pharmaceuticals adsorption with μGACs in tertiary treatment.