This two-week anaerobic batch study evaluated 2,4,6-trinitrotoluene (TNT) removal efficiency from industrial pink water by (1) adsorption on low-cost adsorbent pine bark, and (2) adsorption coupled with TNT biotransformation by specialised microbial communities. Samples of the supernatant and acetonitrile extracts of pine bark were analysed by HPLC, while the composition of the bacterial community of the experimental batches, inocula and pine bark were profiled by high-throughput sequencing the V6 region of the bacterial 16S rRNA gene. Integrated adsorption and biotransformation proved to be the most efficient method for TNT removal from pink water. The type of applied inoculum had a profound effect on TNT removal efficiencies and microbial community structures, which were dominated by phylotypes belonging to the Enterobacteriaceae family. The analysis of acetonitrile extracts of pine bark supported the hypothesis that the microbial community indigenous to pine bark has the ability to degrade TNT.