In small populations and scattered communities, wastewater treatment through vegetation filters (VFs), a nature-based solution, has proved to be feasible, especially for nutrient and organic matter removal. However, the presence of pharmaceuticals in wastewater and their potential to infiltrate through the vadose zone and reach groundwater is a drawback in the evaluation of VF performances. Soil amended with readily labile carbon sources, such as woodchips, enhances microbial activity and sorption processes, which could improve pharmaceutical attenuation in VFs. The present study aims to assess if woodchip amendments to a VF’s soil are able to abate concentrations of selected pharmaceuticals in the infiltrating water by quantitatively describing the occurring processes through reactive transport modelling. Thus, a column experiment using soil collected from an operating VF and poplar woodchips was conducted, alongside a column containing only soil used as reference. The pharmaceuticals acetaminophen, naproxen, atenolol, caffeine, carbamazepine, ketoprofen and sulfamethoxazole were applied daily to the column inlet, mimicking a real irrigation pattern and periodically measured in the effluent. Ketoprofen was the only injected pharmaceutical that reached the column outlet of both systems within the experimental timeframe. The absence of acetaminophen, atenolol, caffeine, carbamazepine, naproxen and sulfamethoxazole in both column outlets indicates that they were attenuated even without woodchips. However, the presence of 10,11-epoxy carbamazepine and atenolol acid as transformation products (TPs) suggests that incomplete degradation also occurs and that the effect of the amendment on the infiltration of TPs is compound-specific. Modelling allowed us to generate breakthrough curves of ketoprofen in both columns and to obtain transport parameters during infiltration. Woodchip-amended columns exhibited Kd and μw values from one to two orders of magnitude higher compared to soil column. This augmentation of sorption and biodegradation processes significantly enhanced the removal of ketoprofen to over 96%.