Along 3 replicate transects, sediments were sampled from a subtidal sandbank in Cockburn Sound, Western Australia, at 4 depths: 1.5, 4 and 8 m and at 14 m on the flat at the base of the bank. Pulse amplitude modulated (PAM) fluorescence, fluxes of oxygen and inorganic nutrients, N2 fixation and denitrification were measured and sediments analysed for granulometry, pigments, fatty acids, neutral lipids, organic C and total N. There were 2 functional depth zones: 1.5 ~ <4, and ≥4 m. At 1.5 m, chl a concentration was 42.3 mg m–2 (1.83 SE, n = 12), sediments were net heterotrophic, and there were effluxes of inorganic nutrients in the light and uptake in the dark. The 2 intermediate depths had benthic microalgal (BMA) biomass around 88 mg m–2 chl a, and mean gross primary productivity of 2.23 mmol O2 m–2 h–1. At 14 m, chl a concentration was 75 mg m–2, and sediments were net autotrophic. Sediment–water exchanges of inorganic nutrients were dominated by NH4, with maximum efflux from the sediment (1044 µmol m–2 d–1) at 8 m and maximum uptake (539 µmol m–2 d–1) at 4 m. At 1.5 m depth, there was a marked discontinuity in most parameters as the microbial community metabolism and cycling of nutrients between the sediment and water column were altered in conditions of more frequent wave disturbance. At depths ≥4 m, we observed greater amounts of biomass and more primary productivity, but net exchanges of inorganic nutrients were remarkably consistent at all depths from 1.5 to 14 m.