Per- and polyfluoroalkyl substances (PFAS) are emerging organic pollutants and can occur in surface and groundwater. To identify the degree of pollution in surface water with PFAS, often targeted HPLC–ESI–MS/MS has been employed in which commonly 30–40 compounds are analyzed. However, other PFAS and organofluorines remain undetected. We sampled surface water of the river Spree and the Teltow Canal in Berlin, Germany, which are affected by the effluent discharge of wastewater treatment plants. Here, we employed high-resolution continuum source graphite furnace molecular absorption spectrometry (HR-CS-GFMAS) for measuring extractable organofluorines (EOF) and compared in a mass balance approach the total fluorine to the identified and quantified PFAS from the targeted analysis. The analysis highlights that the EOF are in the range expected for an urban river system (Winchell et al. in Sci Total Environ 774, 2021). However, downstream of an effluent discharge, the EOF increased by one order of magnitude, e.g., 40.3 to 574 ng F L−1, along the Teltow Canal. From our target analytes, mostly short-chained perfluorinated carboxylic acids and sulfonates occur in the water, which however makes up less than 10% of the EOF. The increase in EOF in the Teltow Canal correlates well with the increase of perfluorohexanoic acid (PFHxA), indicating that PFHxA is characteristic for the discharged EOF but not responsible for the increase. Hence, it points to PFHxA precursor discharge. The study highlights that EOF screening using HR-CS-GFMAS is necessary to identify the full scale of pollution with regard to PFAS and other organofluorines such as pharmaceutical compounds from the effluent of WWTPs.