Reversed-phase liquid chromatography (RPLC) used for water analysis is not ideal for the analysis of highly polar and ionic contaminants because of low retention. Capillary electrophoresis (CE), on the other hand, is perfectly suited for the separation of ionic compounds but rarely applied in environmental analysis due to the weak concentration sensitivity when coupled to mass spectrometry (MS). However, novel interface designs and MS technology strongly improve the sensitivity. Here, a method is presented enabling the screening of anionic micropollutants in drinking water without sample pretreatment by coupling of CE to an Orbitrap mass spectrometer by a nanoflow sheath liquid interface. Targeted analysis of halogenated acetic acids, trifluoromethanesulfonic acid, and perfluorooctanoic and perfluorooctanesulfonic acid was conducted in drinking water samples which were chlorinated for disinfection. A bare fused silica capillary with an optimized background electrolyte (BGE) for separation consisting of 10% acetic acid with 10% isopropanol with large volume sample injection and optimized interface parameters offer limits of quantification in the range of < 0.1 to 0.5 μg/L with good linearity (R 2 > 0.993) and repeatability (14% standard deviation in area). Concentrations of the target analytes ranged from 0.1 to 6.2 μg/L in the water samples. Masses corresponding to halogenated methanesulfonic acids have been found as suspects and were subsequently verified by standards. Mono-, dichloro-, and bromochloro methanesulfonic acid were quantified in a range of 0.2 to 3.6 μg/L. Furthermore, five sulfonic acids, four organosulfates, and the artificial sweeteners acesulfame and cyclamate as well as inorganics such as halides, halogenates, phosphate, and sulfate could be determined as suspects among more than 300 features in a non-targeted screening. Overall, this approach demonstrates the great potential of CE-nanoESI-MS for the screening of ionic contaminants in environmental samples, complementary to chromatographic approaches.