Notes: 1. The objectives of the present work were: (a) to evaluate the effects of the development and the presence of a photosynthetically active algal biofilm on chemical fluxes and processes at the sediment–water interface; (b) to measure the effects of the biofilm on chemical concentration gradients in the bulk sediment; and (c) to monitor pH and dissolved oxygen concentration in the biofilm, and through the sediment–water interface using microelectrodes.2. Two experiments were performed over a period of 8 weeks using a recirculating fluvarium channel containing river sediments with an exposed surface of 0.2 m2 and 20 dm3 of overlying solution. The first experiment was in darkness with minimal effects of a photosynthetically active biofilm. The second experiment in natural light produced a complex photosynthetic biofilm involving a succession of diatoms, green algae and cyanobacteria.3. The solution overlying the biofilm was monitored continuously for dissolved calcium, silicon, phosphorus, alkalinity and oxygen, as well as conductivity, temperature and pH. The surface of the sediment was also monitored for biological and physical changes as the biofilm developed. The overlying solution was analysed over a period of 48 h at 2-h intervals to examine the effects of a well-developed algal biofilm. At the end of the 48 h, pH and oxygen microelectrodes were used to measure gradients above and through the biofilm, and porewaters were analysed from sediments which had been longitudinally sectioned at a maximum depth resolution of 0.5 mm.4. Biofilm development had a large influence on the composition of the overlying solution and the development of vertical concentration gradients of solutes in the porewater. Once a diatom community was established, the concentration of dissolved silicon was low (〈 40 μm), with all the silicon diffusing from the underlying sediment being consumed in the biofilm (≈ 0.026 μmol m−2 s−1 at the end of the experiment).5. The concentrations of calcium, alkalinity and phosphorus in digested sediment increased near the sediment–water interface. X-ray diffraction analysis showed that calcite was formed at the surface. Estimation of the fluxes of alkalinity and calcium in the overlying solution were consistent with calcite formation during daylight and possible dissolution in darkness. The maximum precipitation flux of calcium was 0.87 μmol m−2 s−1 and the maximum net release flux was 0.89 μmol m−2 s−1.6. The net loss of soluble reactive phosphorus from the overlying solution measured over the intensive sampling period of 48 h is consistent with a coprecipitation mechanism and a surface density of phosphorus included in the lattice of calcite of 0.097 μmol m−2. Processes in the biofilm rather than diffusion from the sediment porewater control chemical fluxes of calcium, alkalinity and phosphorus from the sediment to the overlying water.