Pharmaceuticals, once ingested, are commonly metabolized in the body into more polar and soluble forms. These compounds might not be completely removed in the wastewater treatment plants and consequently being discharged into the aquatic ecosystem. In this work, a multi-class sensitive method for the analysis of 21 compounds, including 7 widely consumed pharmaceuticals and 14 relevant metabolites, has been developed based on the use of UHPLC-MS/MS in selected reaction monitoring (SRM) mode. The method was validated in six surface waters (SW) and six effluent wastewaters (EWW) at realistic concentration levels that can be found in waters. The optimized method was applied to the analysis of different types of water samples (rivers, lakes and effluent wastewater), detecting nearly all the parent compounds and metabolites investigated in this work. This fact illustrates that not only pharmaceuticals but also their metabolites are commonly present in these types of waters. Analytical research and monitoring programs should be directed not only towards parent pharmaceuticals but also towards relevant metabolites to have a realistic overview of the impact of pharmaceuticals in the aquatic environment.