To improve bacterial removal, a traditional stormwater biofilter can be augmented with biochar, but it is unknown whether bacterial removal remains consistent as the biochar weathers during intermittent exposure to stormwater under dry-wet and freeze-thaw cycles. To examine the effect of weathering on bacterial removal capacity of biochar, we subjected biochar-augmented sand filters (or simplified biofilters) to multiple freeze-thaw or dry-wet cycles for a month and then compared their bacterial removal capacity with the removal capacity of unweathered biofilters. To isolate the effect of physical and chemical weathering processes from that of biological processes, the biofilters were operated without any developed biofilm. Biochar particles were mobilized during intermittent infiltration of stormwater, but the mobilization depended on temperature and antecedent conditions. During stormwater infiltration without intermediate drying, exposure to natural organic matter (NOM) in the stormwater decreased the bacterial removal capacity of biochar, partly due to exhaustion of attachment sites by NOM adsorption. In contrast, exposure to the same amount of NOM during stormwater infiltration with intermediate drying resulted in higher bacterial removal. This result suggests that dry-wet cycles may enhance recovery of the previously exhausted attachment sites, possibly due to diffusion of NOM from biochar surfaces into intraparticle pores during intermediate drying periods. Overall, these results indicate that physical weathering has net positive effect on bacterial removal by biochar-augmented biofilters.