Chalk streams provide unique, environmentally important habitats, but are particularly susceptible to human activities, such as water abstraction, fish farming and intensive agricultural activity on their fertile flood-meadows, resulting in increased nutrient concentrations. Weekly phosphorus, nitrate, dissolved silicon, chloride and flow measurements were made at nine sites along a 32 km stretch of the River Frome and its tributaries, over a 15 month period. The stretch was divided into two sections (termed the middle and lower reach) and mass balances were calculated for each determinand by totalling the inputs from upstream, tributaries, sewage treatment works and an estimate of groundwater input, and subtracting this from the load exported from each reach. Phosphorus and nitrate were retained within the river channel during the summer months, due to bioaccumulation into river biota and adsorption of phosphorus to bed sediments. During the autumn to spring periods, there was a net export, attributed to increased diffuse inputs from the catchment during storms, decomposition of channel biomass and remobilisation of phosphorus from the bed sediment. This seasonality of retention and remobilisation was higher in the lower reach than the middle reach, which was attributed to downstream changes in land use and fine sediment availability. Silicon showed much less seasonality, but did have periods of rapid retention in spring, due to diatom uptake within the river channel, and a subsequent release from the bed sediments during storm events. Chloride did not produce a seasonal pattern, indicating that the observed phosphorus and nitrate seasonality was a product of annual variation in diffuse inputs and internal riverine processes, rather than an artefact of sampling, flow gauging and analytical errors.