The determination of acidic pharmaceutical and endocrine disrupting compounds at low ng/L levels in surface and wastewater requires highly selective and sensitive analytical procedures. Therefore, the water samples under study were prepared by means of solid phase extraction (SPE) for analyte enrichment and clean up. Prior to GC-NCI-MS, the polar analytes were derivatized using pentafluorobenzyl bromide. The performance of this analytical method has been revealed in fortification experiments by limits of detection ranging from 0.01 to 0.2 ng/L for, e. g., ibuprofen and 17a-ethinylestradiol, respectively. SPE may be the most rate determining step of the analytical procedure. Therefore, the performance of SPE disks and cartridges was additionally compared. Method evaluation demonstrated that even complex sample matrices, such as model wastewater or even synthetic humic acids, did not interfere with the quantification and identification of target analytes. The performance of the analytical method developed for water monitoring was further emphasized by the investigation of surface water of the River Saale and effluents of the wastewater treatment plant (WWTP) at Halle, Saxony-Anhalt, Germany. In those samples, acidic pharmaceuticals and corresponding metabolites occurred at 0.1 ng/L for clofibric acid up to 498 ng/L for bezafibrate. Technical nonylphenol and bisphenol A were found in every water sample. Meanwhile, 17a-ethinylestradiol was determined only in one WWTP effluent sample at 1 ng/L.