The patterns in nitrate and phosphorus sources, loads and concentrations in a groundwater-dominated lowland catchment, the Hampshire Avon, are examined and water quality signatures are used to identify a typology of headwater stream types. The major separations in water quality are linked to geology and groundwater chemistry as modified by the impacts of point source sewage effluents. The water quality of the major tributaries and the main stem of the River Avon are linked to the relative contributions of these source types, the impact of further direct effluent inputs to the main channel and in-stream processing. The tributaries and main stem of the Avon act as net sinks for total reactive phosphorus (TRP). Low concentrations of TRP were found in the Chalk groundwater and the groundwater system acts as an efficient buffer, removing and retaining TRP from water draining from the catchment surface into the aquifer. Thermodynamic analysis of calcium carbonate (CaCO3) solubility controls indicates that this natural 'self-cleansing mechanism' system within the groundwater may be directly linked to CaCO3-P co-precipitation within the aquifer matrix.