Changes in concentrations of soluble reactive phosphorus (SRP), excess partial pressure of carbon dioxide (EpCO2), and chlorophyll-a were examined for two rivers in the in the upper Thames catchment: the main river Thames at Wallingford and a chalk stream tributary, the River Kennet. Sampling began in the spring of 1997 and has covered extremes in river flow conditions. During the sampling period there was a dramatic reduction in phosphorus (P) inputs from the introduction of effluent P-treatment at sewage treatment works, as a result of the EU Urban Wastewater Treatment Directive. Despite major reductions in baseflow SRP concentrations in the River Kennet, from around 700 μg-P L−1to around 100 μg-P L−1, observations of aquatic plant communities indicate overall degradation in ecological quality since effluent P-treatment was introduced. The degradation was associated with a spring and summer decline in growth of Ranunculus, a macrophyte of high conservation value in chalk streams, particularly from 2000 onwards, linked to shading by epiphytic algae. Although the EpCO2 records indicate a reduction in primary productivity since effluent P-treatment, the River Kennet may have become more sensitive to epiphyte blooms. Episodes of epiphyte proliferation appear to be linked temporally to small increases in SRP concentrations (typically above a 100 μg-P L−1threshold) under summer baseflow conditions. The in-stream system is highly complex and individual processes and causality are difficult to resolve, particularly given changes in river flows linked to background climatic variability and limited availability of biological data. This study demonstrates the need for integrated long-term biological and chemical monitoring of river systems subject to major perturbations to assess timescales required to produce new dynamic equilibria in ecosystem response.