This data set comprises weekly water quality monitoring data of seven sites along the River Thames, UK, and sixteen of its major tributaries from March 2009 to September 2017. 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 and 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 UK Centre for Ecology & Hydrology's Thames Initiative monitoring programme. This work was supported by the Natural Environment Research Council award number NE/R016429/1 as part of the UK-SCAPE programme delivering National Capability.