The application of nitrification and urease inhibitors (NUI) in conjunction with nitrogen (N) fertilizers improves the efficiency of N fertilizers. However, NUI are frequently found in surface waters through leaching or surface runoff. Bank filtration (BF) is considered as a low-cost water treatment system providing high quality water by efficiently removing large amounts of organic micropollutants from surface water. The fate of NUI in managed aquifer recharge systems such as BF is poorly known. The aim of this work was to investigate sorption and degradation of NUI in simulated BF under near-natural conditions. Besides, the effect of NUI on the microbial biomass of slowly growing microorganisms and the role of microbial biomass on NUI removal was investigated. Duplicate sand columns (length 1.7 m) fed with surface water were spiked with a pulse consisting of four nitrification (1,2,4-triazole, dicyanodiamide, 3,4-dimethylpyrazole and 3-methylpyrazole) and two urease inhibitors (n-butyl-thiophosphoric acid triamide and n-(2-nitrophenyl) phosphoric triamide). The average spiking concentration of each NUI was 5 μg/L. Experimental and modeled breakthrough curves of NUI indicated no retardation for any of the inhibitors. Therefore, biodegradation was identified as the main elimination pathway for all substances and was highest in zones of high microbial biomass. Removal of 1,2,4-triazole was 50% and n-butyl-thiophosphoric acid triamide proved to be highly degradable and was completely removed after a hydraulic retention time (HRT) of 24 h. 50% of the mass recovery for nitrification inhibitors except for 3,4-dimethylpyrazole was observed at the effluent (4 days HRT). In addition, a mild effect of NUI on microbial biomass was noted. This study highlights that the degradation of NUI in BF depends on HRT and microbial biomass.