This paper examines the nutrient chemistry and biological quality indices [Mean Trophic Rank (MTR) and Trophic Diatom Index (TDI)] for rivers within the upper Thames basin. The predominant sources of nitrogen within the rivers monitored were diffuse and agricultural in nature. However, phosphorus showed both diffuse and point source signals. MTR surveys undertaken both upstream and downstream of major STWs indicate that these rivers are ‘at risk’ of eutrophication or ‘badly damaged’. MTR surveys also indicate increased trophic status downstream of STWs, whereas TDI does not indicate such a consistent pattern. Phosphorus treatment at selected major sewage treatment works in the upper Thames basin resulted in significant reductions in in-stream P concentrations and reductions in fluxes by a half to two thirds. However, the effects of P-reduction on in-stream ecology (measured as MTR and TDI) were more difficult to ascribe, owing to: (1) the high variability in river flow rates experienced since P-reduction was introduced; (2) lag effects related to P stores in river bed sediments; and (3) diffuse and smaller point source inputs upstream. The results of this study indicate that control of upstream sources of phosphorus may prove critical in improving the biological quality status of UK lowland rivers, including ecological responses to P-source controls on the major sewage treatment works downstream. Upstream sources include both diffuse (agricultural) sources and small point source inputs which, at present, are not classified as ‘qualifying discharges’ under the Urban Wastewater Treatment Directive (UWWTD) and are thus not subject to phosphorus control measures. These results are of relevance for integrated, sustainable management and protection of European freshwater resources, particularly in terms of new ecological targets for water quality management under the new Water Framework Directive.