Freshwater systems are facing a number of pressures due to the inputs of polar organic contaminants from a range of sources including agriculture, domestic and industry. The River Itchen and River Test are two sensitive chalk streams in Southern England that are experiencing a decline in invertebrate communities. We used Chemcatcher passive samplers to measure time-weighted average concentrations (14 days) of polar pollutants at nine sites on the River Itchen and eight sites on the River Test over a 12-month period. Sampler extracts were analysed using a targeted LC/MS method. In total, 121 plant protection products and pharmaceutical and personal care products were quantified (range of log Kow from - 1.5 to 7). Concentrations (sub ng L−1 to >500 ng L−1) in both rivers showed spatial and temporal variations. A greater number of compounds and higher concentrations were found in the River Test. The chemical profile was dominated by inputs from wastewater treatment plants and legacy plant protection products. On the River Itchen, high concentrations (∼100 ng L−1) of caffeine were observed directly downstream of a fish farm. Using the NORMAN database, the predicted no effect concentration (PNEC) freshwater values were exceeded by only five contaminants (2-hydroxy-terbuthylazine, alprazolam, azithromycin, diclofenac and imidacloprid). In addition, venlafaxine was detected above its EU Watch List concentration. These exceedances were mainly downstream of direct inputs from treatment plants. These compounds are known to have ecotoxicological effects on a range of aquatic biota including macroinvertebrates. Of concern is the ubiquitous presence of the ectoparasiticide imidacloprid, highlighting the need to control its use. The impact of the cocktail of pollutants found in this study on the long-term effects on chalk stream ecosystems remains unknown and needs further investigation. Display omitted •Chemcatcher used to sequester polar pollutants in river catchments in southern England.•121 compounds quantified using a targeted mass spectrometric workflow.•Waste water treatment plant effluents were the main contributor of pharmaceuticals.•Five compounds were found at or above their predicted no effect concentrations.•Presence of imidacloprid could impact macroinvertebrate communities.