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Background Exposure to disinfection by-products (DBPs) in drinking water and chlorinated swimming pools are associated with adverse health outcomes, but biological mechanisms remain poorly understood. Objectives Evaluate short-term changes in metabolic profiles in response to DBP exposure while swimming in a chlorinated pool. Materials and methods The PISCINA-II study (EXPOsOMICS project) includes 60 volunteers swimming 40 min in an indoor pool. Levels of most common DBPs were measured in water and in exhaled breath before and after swimming. Blood samples, collected before and 2 h after swimming, were used for metabolic profiling by liquid-chromatography coupled to high-resolution mass-spectrometry. Metabolome-wide association between DBP exposures and each metabolic feature was evaluated using multivariate normal (MVN) models. Sensitivity analyses and compound annotation were conducted. Results Exposure levels of all DBPs in exhaled breath were higher after the experiment. A total of 6,471 metabolic features were detected and 293 features were associated with at least one DBP in exhaled breath following Bonferroni correction. A total of 333 metabolic features were associated to at least one DBP measured in water or urine. Uptake of DBPs and physical activity were strongly correlated and mutual adjustment reduced the number of statistically significant associations. From the 293 features, 20 could be identified corresponding to 13 metabolites including compounds in the tryptophan metabolism pathway. Conclusion Our study identified numerous molecular changes following a swim in a chlorinated pool. While we could not explicitly evaluate which experiment-related factors induced these associations, molecular characterization highlighted metabolic features associated with exposure changes during swimming. © 2017 The Authors, This work was supported by the grant FP7 of the European Commission ‘Enhanced exposure assessment and omic profiling for high priority environmental exposures in Europe’ (EXPOsOMICS grant 308610 to PV). The Centre for Environment and Health is supported by the Medical Research Council and Public Health England (MR/L01341X/1). Marc Chadeau-Hyam acknowledges support from Cancer Research UK, Population Research Committee Project grant (‘Mechanomics’ project #22184 to MC-H).