The effects of pharmaceuticals and personal care products (PPCPs) on aquatic organisms represent a significant current concern. Herein, a targeted metabolomics approach using liquid chromatography-high resolution mass spectrometry (LC-HRMS) is presented to characterise concentration changes in 29 selected metabolites following exposures of aquatic invertebrates, Gammarus pulex, to pharmaceuticals. Method performance revealed excellent linearity (R2 > 0.99), precision (0.1–19%) and lower instrumental limits of detection (0.002–0.20 ng) for all metabolites studied. Three pharmaceuticals were selected representing the low, middle and high range of measured acute measured toxicities (of a total of 26 compounds). Gammarids were exposed to both the no-observed-adverse-effect-level (NOAEL) and the lowest-observed-adverse-effect-level (LOAEL) of triclosan (0.1 and 0.3 mg L− 1), nimesulide (0.5 and 1.4 mg L− 1) and propranolol (100 and 153 mg L− 1) over 24 h. Quantitative metabolite profiling was then performed. Significant changes in metabolite concentrations relative to controls are presented and display distinct clustered trends for each pharmaceutical. Approximately 37% (triclosan), 33% (nimesulide) and 46% (propranolol) of metabolites showed statistically significant time-related effects. Observed changes are also discussed with respect to internal concentrations of the three pharmaceuticals measured using a method based on pulverised liquid extraction, solid phase extraction and LC-MS/MS. Potential metabolic pathways that may be affected by such exposures are also discussed. This represents the first study focussing on quantitative, targeted metabolomics of this lower trophic level benthic invertebrate that may elucidate biomarkers for future risk assessment.