In this paper we report the results of an experimental study of periphyton–flow interactions conducted in a specially designed outdoor hydraulic flume. ‘Periphyton’ is a collective term for the micro-organisms which grow on stream beds, and includes algae, bacteria, and fungi, with algae usually the dominant and most conspicuous component. The main goals of the study are to identify potential effects of periphyton–flow interactions as well as the potential mechanisms of mass transfer in the near-bed region, which could influence periphyton growth and losses. The main results of the study may be summarized as follows.

A linear velocity distribution in the interfacial sublayer (i.e. below the roughness tops), and a logarithmic distribution above the roughness tops appeared to be reasonable approximations for both flow types, with and without periphyton on the bed. However, the appearance of periphyton on a rough bed shifts the origin of the bed upwards, increases the roughness length zo by 16–21%, and reduces the ratio of the mean velocity at the level of roughness tops to the shear velocity by ≈30%. In general, below the roughness tops the periphyton suppresses the mean velocities, the turbulent stresses, turbulence intensities, and vertical turbulent fluxes of the turbulent energy and turbulent shear stresses.

It was found that in flows without periphyton large-scale eddies successfully penetrate the interfacial sublayer. However, tufts of periphyton on the tops of the roughness elements significantly weaken the penetration processes leading to spatial de-correlation in the velocity field within the interfacial sublayer. The appearance of periphyton on the bed does not change appreciably the velocity spectra above the roughness tops but reduces the total spectral energy and generates a wide spectral peak in the interfacial sublayer. Most probably, this peak is formed by penetration of sweep events into the interfacial sublayer, ‘filtered’ by the periphyton tufts. Thus, sweep events may be the main mechanism responsible for the delivery of nutrients from the outer region to the biologically active interfacial sublayer. The potential effects of flow properties on the periphyton community are also discussed.