Variations in phosphorus (P) concentrations in an agriculturally impacted river draining a Chalk aquifer and an associated canal in the west of the Thames Basin, southern England are examined and linked to agricultural and sewage sources and within river/canal process controls. The study area comprises the River Dun, the adjacent River Kennet and the Kennet and Avon (K&A) Canal. Large seasonal variations are observed for soluble reactive phosphorus (SRP) and dissolved silicon (Si) with low concentrations in the spring and summer times when biological activity is high. The K&A Canal shows the largest SRP and Si concentration declines. This reflects high biological activity coupled with higher temperatures and higher water residence times. The extent of SRP removal is examined in relation to organic (uptake/release with phytoplankton growth/decay) and, to a lesser extent, inorganic (SRP coprecipitation with calcite) mechanisms. Boron (B) is used as a tracer of sewage sources. Agricultural inputs of both dissolved and particulate P (PP) can be important particularly under conditions where the catchment is wet and near surface/overland flow is important: sewage treatment works effluent and septic tank discharges to groundwater also probably provide a major component of the SRP occurring within the water column. The canal, and to a lesser extent the river, acts as sink for P in sewage effluent sources due to the high biological activity especially during the spring and summer. The aquifer probably acts as a major sink for agricultural and septic tank inputs of P.