Stream-bed sediments from three paired catchments, each draining a lower agricultural intensity system and a higher agricultural intensity system, were analysed for (a) total P (TP), (b) bioavailable-P (Resin-P), (c) equilibrium phosphorus concentration (EPC0), and (d) degree of phosphorus saturation (DPS). The influence of agriculture on sediment P was explored within the context of other key variables that may control the sediment P concentrations such as particle size, Fe, Ca and organic matter content, and in terms of potential implications of sediment P to in-stream biota. TP concentrations, EPC0, and the proportion of fine sediment were highest at the sites with the greater agricultural impact. Higher concentrations of bioavailable-P were also found in higher intensity agricultural systems. However, the highest concentrations of bioavailable-P were found at sites with point source inputs. Sites with high Fe concentrations had higher TP concentrations relative to agricultural intensity, but also had lower DPS values, illustrating that the sediment still had the capacity to take up P in a strongly bound form. The results from this study show that higher risk agricultural practices (intensive arable production and dairy and beef production) can lead either directly, or indirectly through increased inputs of fine sediment, to increased sediment TP concentrations. The importance of geochemical and physical controls on the bed sediments’ capacity to mitigate high P inputs in headwater lowland streams, especially under low flows and times of eutrophication risk in spring and summer is illustrated.