A sensitive and selective analytical method, based on online solid phase extraction coupled to LC–MS/MS, was developed and validated to determine traces of several recently introduced fungicides in surface water and wastewater. The list of target analytes included eight succinate dehydrogenase inhibitors (bixafen, boscalid, fluopyram, flutolanil, fluxapyroxad, isopyrazam, penflufen, and penthiopyrad), and two other fungicides with different modes of action, fenpyrazamine and fluopicolide. Detection and quantification limits in various matrices were in the range of 0.1 to 2 ng/L and 0.5 to 10 ng/L, respectively. Moderate signal suppression was observed in surface water (≤ 15%) and wastewater (≤ 25%) and was well compensated by the selected internal standard. The intra- and inter-day precision were generally <10% and <20%, respectively. The applicability of the method was demonstrated in a study on the occurrence of fungicides in the river Glatt, Switzerland, that drains a catchment area of 419 km2 with a substantial proportion of agricultural land. Of the studied compounds, only boscalid and fluopicolide were detected in flow-proportional weekly composite samples, generally at low concentrations up to 15 and 5 ng/L, respectively. While fluopicolide was detected in only 30% of the samples above the LOD of 0.5 ng/L, boscalid was detected in all samples analyzed between March and October 2012.