Estimates of clearance rates (CR) of Cerastoderma edule (300 ind. m−2) as a function of free-stream current velocity (U) (from 5 to 40 cm s−1) were compared between a small annular (60 l) and a large racetrack (8850 l) flume with different hydrodynamic conditions. Results showed that the flumes differ considerably in their hydrodynamic characteristics. The relationship between CR and U is different in the two flume tanks, however there appears to be a straightforward unimodal trend between CR and shear velocity (U*). It was found that the cockles themselves influence the benthic boundary layer (BBL) characteristics, by causing steeper velocity gradients and increasing the mixing over the cockle bed compared to bare sediment. This provides new evidence on how endobenthic organisms can affect the BBL. However, the influence of CR on U* could not be quantified because these parameters have interactive effects that cannot be dissociated.