This data set comprises of weekly water quality monitoring data of seven sites along the River Thames, UK, and fifteen of its major tributaries from February 2009 to February 2013. Parameters measured were phosphorus and nitrogen species, dissolved reactive silicon, water temperature, pH, Gran alkalinity, suspended solids, chlorophyll and major dissolved anions (fluoride, chloride, bromide, sulphate) and cations (sodium, potassium, calcium, magnesium, boron). Dissolved and total iron, manganese, zinc, copper concentrations have also been produced from August 2010 to February 2013. The accompanying daily river flow data are also supplied. Samples were taken as part of the Centre for Ecology & Hydrology’s Thames Initiative monitoring programme. ; Methods ; All water samples were collected by fieldworkers from the Centre for Ecology & Hydrology (CEH), Wallingford. All chemical analysis was carried out by the Nutrient Chemistry Laboratories at CEH Wallingford. Daily mean flow data that accompany the data set were produced by the Environment Agency, and downloaded from the National River Flow Archive in January 2017. Interpretation of this data set can be found in the following papers: [1] Bowes MJ, Gozzard E, Johnson AC, Scarlett PM, Roberts C, Read DS, et al. Spatial and temporal changes in chlorophyll-a concentrations in the River Thames basin, UK: Are phosphorus concentrations beginning to limit phytoplankton biomass? Sci Total Environ (2012) 426: 45-55. [2] Bowes MJ, Jarvie HP, Naden PS, Old GH, Scarlett PM, Roberts C, et al. Identifying priorities for nutrient mitigation using river concentration–flow relationships: The Thames basin, UK. J of Hydrol (2014) 517: 1-12. [3] Bowes MJ, Loewenthal M, Read DS, Hutchins MG, Prudhomme C, Armstrong LK, et al. Identifying multiple stressor controls on phytoplankton dynamics in the River Thames (UK) using high-frequency water quality data. Sci Total Environ (2016) 569–570: 1489-1499.