The impact of organic loading rate (OLR) on carbonaceous materials and ammonia removal was assessed in bench scale rotating media biofilm reactors treating real wastewater. Media composition influences biofilm structure and therefore performance. Here, plastic mesh, reticulated coarse foam and fine foam media were operated concurrently at OLRs of 15, 35 and 60 g sCOD m−2d−1 in three bench scale shaft mounted advanced reactor technology (SMART) reactors. The sCOD removal rate increased with loading from 6 to 25 g sCOD m−2d−1 (P < 0.001). At 35 g BOD5m−2d−1, more than double the arbitrary OLR limit of normal nitrifying conditions (15 g BOD5m−2d−1); the removal efficiency of NH4-N was 82 ± 5, 27 ± 19 and 39 ± 8% for the mesh, coarse foam and fine foam media, respectively. Increasing the OLR to 35 gm−2d−1 decreased NH4-N removal efficiency to 38 ± 6, 21 ± 4 and 21 ± 6%, respectively. The mesh media achieved the highest stable NH4+-N removal rate of 6.5 ± 1.6 gm−2d−1 at a sCOD loading of 35 g sCOD m−2d−1. Viable bacterial numbers decreased with increasing OLR from 2 × 1010–4 × 109 cells per ml of biofilm from the low to high loading, suggesting an accumulation of inert non-viable biomass with higher OLR. Increasing the OLR in permeable media is of practical benefit for high rate carbonaceous materials and ammonia removal in the pretreatment of wastewater.