This study was undertaken to investigate the role of primary substrate composition and concentration on the attenuation of biodegradable emerging trace organic chemicals (TOrCs) in simulated managed aquifer recharge (MAR) systems. Four sets of soil columns were established in the laboratory, each receiving synthetic feed solutions comprising different ratios and concentrations of peptone-yeast and humic acid as the primary substrate to investigate the effect on removal of six TOrCs (atenolol, caffeine, diclofenac, gemfibrozil, primidone, and trimethoprim). Based on abiotic control experiments, adsorption was not identified as a significant attenuation mechanism for primidone, gemfibrozil and diclofenac. Caffeine, atenolol and trimethoprim displayed initial adsorptive losses, however, adsorption coefficients derived from batch tests confirmed that adsorption was limited and in the long-term experiment, biodegradation was the dominant attenuation process. Within a travel time of 16 h, caffeine – an easily degradable compound exhibited removal exceeding 75% regardless of composition or concentration of the primary substrate. Primidone – a poorly degradable compound, showed no removal in any column regardless of the nature of the primary substrate. The composition and concentration of the primary substrate, however, had an effect on attenuation of moderately degradable TOrCs, such as atenolol, gemfibrozil and diclofenac, with the primary substrate composition seeming to have a larger impact on TOrC attenuation than its concentration. When the primary substrate consisted mainly of refractory substrate (humic acid), higher removal of the moderately degradable TOrCs was observed. The microbial communities in the columns receiving more refractory carbon, were noted to be more diverse and hence likely able to express a wider range of enzymes, which were more suitable for TOrC transformation. The effect of the primary substrate on microbial community composition, diversity and gene expression potential confirmed its influence on TOrC degradation.