Livestock animals are commonly treated with veterinary pharmaceuticals (VPs), and their residues often enter the environment through manure applied to soil. A fraction of these residues may be further transported to surface waters through intricate transport mechanisms. Here, we examine the temporal dynamics of VPs in lowland surface waters of an agricultural catchment in the Netherlands, utilizing information on VPs concentrations in manure and surface water measurements. We develop a parsimonious catchment-scale transport model for VPs that is based on time-variable water transit time distributions. The transport model considers multiple processes experienced by the VPs during their transfer to the stream network, including evapoconcentration, sorption and degradation. Our results suggest that, despite the mean water transit times of several years typical of lowland catchments, as well as relatively strong VP sorption or rapid degradation, detectable amounts of VPs in the order of 1–10 ng/L may reach the stream ecosystem through fast flowpaths characterized by short transit times. Therefore, VPs may be used as tracers of short water flowpaths in agricultural catchments.