Sediments composed of mixed cohesive clay and non-cohesive sand are widespread in a range of aquatic environments. The dynamics of ripples in mixed sand–clay substrates have been studied under pure current and pure wave conditions. However, the effect of cohesive clay on ripple development under combined currents and waves has not been examined, even though combined flows are common in estuaries, particularly during storms. Based on a series of large flume experiments, we identified robust inverse relationships between initial bed clay content, C0, and wave–current ripple growth rates. The experimental results also revealed two distinct types of equilibrium combined–flow ripples on mixed sand–clay beds: (a) large asymmetrical ripples with dimensions and plan geometries comparable to clean-sand counterparts for C0 ≤ 10.6%; and (b) small, flat ripples for C0 > 11%. The increase in bed cohesion contributed to this discontinuity, expressed most clearly in a sharp reduction in equilibrium ripple height, and thus a significant reduction in bed roughness, which implies that the performance of existing ripple predictors can be improved by the incorporation of this physical cohesive effect. For C0 ≤ 10.6%, strong clay winnowing efficiency under combined flows resulted in the formation of equilibrium clean-sand ripples and clay loss at depths far below the ripple base. In natural environments, this ‘deep cleaning’ of bed clay may cause a concurrent sudden release of a large amount of pollutants during storms, leading to a sudden reduction in post-storm resistance to erosion of mixed sand–clay substrates.