Trifluoroacetate (TFA) is a contaminant from various human sources. The degradation of fluorinated gases in the atmosphere leads to a ubiquitous input through precipitation. Degradation of certain agricultural pesticides and wastewater-borne pharmaceuticals adds to the amount of TFA pollution. Once released into the aquatic environment, TFA is nearly conservative due to its negative charge, high water solubility, and absence of degradation pathways. Consequently, TFA concentrations in the environment are constantly increasing, following the production of precursor substances. Previous studies suggested the accumulation of TFA in plants and its retention in organic soil. This knowledge, however, is based on a small number of environmental samples or laboratory experiments. Catchment-scale studies are so far missing. In particular, hydrological processes controlling the retention and mobilization of TFA are poorly understood. Therefore, we analyzed a two-year dataset of weekly water samples for major ions and isotope tracers with TFA in the mountainous Dreisam catchment (Black Forest, Germany). We sampled precipitation, the discharge of three nested catchments, and a hillslope spring. A balancing approach suggested that TFA was not permanently retained in forested headwaters. Therefore, we were able to estimate evapotranspiration in the sub-catchments from two years of TFA concentrations in streamflow. In agricultural areas, we found a surplus of TFA, which totaled an annual input of 11.4 ± 3.9 kg km^-² for arable land. A correlation analysis using environmental tracers, combined with knowledge of runoff generation in the study catchment, suggested that previously retained TFA was flushed from soils under wet conditions, with subsurface stormflow serving as a primary transport path. These findings indicate that TFA concentrations in soils may be higher than average concentrations found in rain or streamflow. Therefore, future research should focus on TFA retention in the unsaturated zone.