The process of bank filtration acts as a barrier against many anthropogenic micropollutants, such as pharmaceuticals and industrial products, leading to a substantial improvement of groundwater quality. The performance of this barrier is, however, affected by seasonal influences and subject to significant temporal changes, which have already been described in the literature. Much less is known about spatial differences when considering one field site. In order to investigate this issue, two undisturbed cores from a well-investigated bank filtration field site were sampled and operated in the course of a column study. The ultimate aim was the identification and quantification of heterogeneities with regard to the biodegradation of 14 wastewater derived micropollutants, amongst others acesulfame, gabapentin, metoprolol, oxypurinol, candesartan, and olmesartan. While six of the compounds entirely persisted, eight compounds were prone to degradation. For those compounds that were subject to degradation, degradation rate constants ranged between 0.2 day−1 (gabapentin) and 31 day−1 (valsartan acid). Further, the rate constants consistently diverged between the distinct cores. In case of the gabapentin metabolite gabapentin-lactam, observed removal rate constants differed by a factor of six between the cores. Experimental data were compared to values calculated according to two structure based prediction models.