Pharmaceutically active compounds have increasingly been detected in groundwater worldwide. Despite constituting a risk for human health and ecosystems, their fate in the environment has still not been exhaustively investigated. This study characterizes the transport behavior of five selected pharmaceutically active compounds (antipyrine, atenolol, caffeine, carbamazepine and sulfamethoxazole) in two sediments (coarse quartz sand and sandy loam) using column experiments with long-term injection of spiked groundwater. Transport parameters were estimated using an analytical reactive transport model. When five selected compounds were injected simultaneously, transport behavior of antipyrine, carbamazepine and the antibiotic sulfamethoxazole were similar to the conservative tracer in both sediments and under varying redox conditions. Atenolol and caffeine were retarded significantly stronger in the sandy loam sediment than in the coarse quartz sand. Biodegradation of caffeine was observed in both sediments after an adaption period and depended on dissolved oxygen. The identification of biodegradation processes was supported by monitoring of intracellular adenosine triphosphate (ATPitc) as a measure for microbial activity. ATPitc was present in varying concentrations in all sediments and was highest when biodegradation of pharmaceuticals, especially caffeine, was observed. When only caffeine and sulfamethoxazole were injected simultaneously, sulfamethoxazole was degraded while caffeine degradation was reduced. The latter seemed to be influenced by low concentrations in dissolved oxygen rather than the presence of the antibiotic sulfamethoxazole. Results of these experiments emphasize the impact on pharmaceutical sorption and (bio)degradation of sediment type and redox conditions, as well as available time for microbial adaption and the combination of pharmaceuticals that are released together into groundwater.