The dataset contains measurements of fluorescein, dopachrome and nitrous oxide production from incubation experiments of streambed sediments. The sediments were collected in five pseudo-replicates from 0 to 10cm depth using a 5cm-diameter AMS slide hammer and trowel at two locations within the Wood Brook, Staffordshire, in June 2015. Samples were collected from two reaches within the stream, a mid-stream sandy reach and a downstream gravel reach. The sediment was used in laboratory incubation experiments to determine rates of fluorescein diacetate (FDA) hydrolysis (total microbial activity), extracellular phenol oxidase activity (recalcitrant carbon uptake) and potential denitrification from sand versus gravel sediments. Also included is the organic matter content of the sediments. The work was funded by the Natural Environment Research Council.