This work examines baseflow nutrient concentrations and loads along two rural Chalk streams, the Pang and Lambourn. Soluble reactive phosphorus (SRP) and boron (B) concentrations in these streams were heavily influenced by point-source inputs and the effects of downstream flow accretion and dilution. Unlike B (which is chemically conservative), SRP loads were also strongly influenced by in-stream processing resulting in uptake of SRP, particularly immediately downstream of sewage effluent discharges, where rates of SRP uptake were highest. For the upper River Pang, up to 80% of SRP loads were lost within 4 km downstream of Compton sewage treatment works (STW) and on the River Lambourn up to 55% of SRP loads were lost within 1.6 km downstream of East Shefford STW. In contrast, nitrate (NO3) concentrations at sites along the Pang and Lambourn were largely controlled by groundwater inputs and plant uptake during periods of high photosynthetic activity in spring and summer and silicon (Si) by diatom uptake in April/May. There were net gains in NO3 loads along the river reaches, as a result of volumetric increases in groundwater discharge, and, compared with SRP, the role of in-stream processing of NO3 appeared low. Examination of SRP exchange by bed sediment and uptake of SRP into algal biofilms indicated that biofilms accounted for only a very small percentage of in-stream P-uptake, but that bed sediment SRP-exchanges had a more important control on baseflow SRP concentrations and loads. Point source P remediation at East Shefford STW, by removal of P from final effluent (P-stripping), resulted in 70–90% reductions in river-water SRP loads. After introduction of P-stripping at East Shefford STW, bed sediments immediately downstream of the STW switched from being net sinks to net sources of SRP. Our results show that, in the immediate aftermath of P-stripping, bed sediment SRP-release was responsible for a 30 μg-P l−1 rise in river-water SRP along this reach. While this increase in SRP concentration, as a result of bed sediment SRP release, is potentially ecologically significant, it is small in relation to the increase in SRP concentrations from effluent prior to P-stripping, which resulted in increases in SRP concentration of up to 500 μg-P l−1. There was a six-month lag between the introduction of P-stripping at East Shefford STW and bed sediment EPC0 recovering to equilibrium levels with the overlying river water (and thus negligible SRP release). Recovery of bed sediments to equilibrium levels is likely to have occurred as a result of winnowing and removal of high-EPC0 sediment and delivery of lower EPC0 sediment from upstream. Under higher/more variable flow conditions and greater rates of in-channel sediment erosion/delivery, more rapid recovery of bed sediment EPC0 levels following P-stripping might be expected.