Bioremediation 
of pharmaceuticals has gained large research efforts, but there is still a need to improve the performance of bioremediation systems by selecting effective organisms. In this study, we characterized the capability to remove clarithromycin (CLA) and diclofenac (DCF) by the bacteriumStreptomyces rochei, and the fungiPhanerochaete chrysosporiumandTrametes versicolor. The macrolide antibiotic CLA and the non-steroid anti-inflammatory DCF were selected because these are two of the most frequently detected drugs in water bodies. Growth and content of the PhCs and a DCF metabolite (MET) by the energy cropArundo donaxL. were also evaluated under hydroponic conditions. The removal rate (RR) byS. rocheiincreased from 24 to 40% at 10 and 100 µg CLA L−1, respectively, averaged over incubation times. At 144 h, the RR byP. chrysosporiumwas 84%, while byT. versicolorwas 70 and 45% at 10 and 100 CLA µg L−1. The RR byS. rocheidid not exceed 30% at 1 mg DCF L−1and reached 60% at 10 mg DCF L−1, whereas approached 95% and 63% byP. chrysosporiumandT. versicolor, respectively, at both doses. Root biomass and length ofA. donaxwere strongly affected at 100 µg CLA L−1. CLA concentration in roots and shoots increased with the increase of the dose and translocation factor (TF) was about 1. DCF severely affected both shoot fresh weight and root length at the highest dose and concentration in roots and shoots increased with the increase of the dose. DCF concentrations were 16–19 times higher in roots than in shoots, and TF was about 0.1. MET was detected only in roots and its proportion over the parent compound decreased with the increase of the DCF dose. This study highlights the potential contribution ofA. donax and the tested microbial inoculants for improving the effectiveness of bioremediation systems for CLA and DCF removal.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11356-023-27660-4.