Chlorophyll-a and nutrient concentrations were monitored at weekly intervals across 21 river sites throughout the River Thames basin, southern England, between 2009 and 2011. Despite a 90% decrease in soluble reactive phosphorus (SRP) concentration of the lower River Thames since the 1990s, very large phytoplankton blooms still occur. Chlorophyll concentrations were highest in the mid and lower River Thames and the larger tributaries. Lowest chlorophyll concentrations were observed in the smaller tributaries, despite some having very high phosphorus concentrations of over 300μgl−1. There was a strong positive correlation between river length and mean chlorophyll concentration (R2=0.82), and rivers connected to canals had ca. six times greater chlorophyll concentration than ‘natural’ rivers with similar phosphorus concentrations, indicating the importance that residence time has on determining phytoplankton biomass. Phosphorus concentration did have some influence, with phosphorus-enriched rivers having much larger phytoplankton blooms than nutrient-poor rivers of a similar length. Water quality improvements may now be capping chlorophyll peaks in the Rivers Thames and Kennet, due to SRP depletion during the spring/early summer phytoplankton bloom period. Dissolved reactive silicon was also depleted to potentially-limiting concentrations for diatom growth in the River Thames during these phytoplankton blooms, but nitrate remained in excess for all rivers throughout the study period. Other potential mitigation measures, such as increasing riparian shading and reducing residence times by removing impoundments may be needed, alongside phosphorus mitigation, to reduce the magnitude of phytoplankton blooms in the future.