Wave–current ripples that develop on seabeds of mixed non-cohesive sand and cohesive clay are commonplace in coastal and estuarine environments. While laboratory research on ripples forming in these types of mixed-bed environments is relatively limited, it has identified deep cleaning, the removal of clay below the ripple troughs, as an important factor controlling ripple development. New large-scale flume experiments seek to address this sparsity in data by considering two wave-current conditions with 15 initial clay content, C0, ranging from 0 to 18.3%. The experiments record ripple development and pre- and post-experiment bed clay contents, to quantify clay winnowing. The present experiments are combined with previous wave–only, wave–current and current–only experiments to produce a consistent picture of larger and smaller flatter ripples over a range of wave-current conditions and C0. Specifically, the results reveal a sudden decrease in the ripple steepness for C0 > 10.6%, likely associated with a three-20 orders of magnitude decrease in hydraulic conductivity. Accompanying the sudden change in steepness is a gradual linear decrease in wavelength with C0 for C0 > 7.4%. Ultimately, for the highest values of C0, the bed remains flat, but clay winnowing still takes place, albeit at a rate two orders of magnitude lower than for rippled beds. For a given flow, the initiation time, when ripples first appear on a flat bed, increases with increasing C0. This, together with the fact that the bed remains flat for the highest values of C0, 25 demonstrates that the threshold of motion increases with C0. The inferred threshold enhancement, and the occurrence of large and small ripples, is used to construct a new three-dimensional phase diagram of bed characteristics involving the wave and current Shields parameters and C0, which has important implications for morphodynamic modelling.