Mixtures of cohesive clay and noncohesive sand are widespread in many aquatic environments. Ripple dynamics in sand-clay mixtures have been studied under current-alone and wave-alone conditions but not combined wave-current conditions, despite their prevalence in estuaries and the coastal zone. The present flume experiments examine the effect of initial clay content, C 0, on ripples by considering a single wave-current condition and, for the first time, quantify how changing clay content of substrate impacts ripple dimensions during development. The results show inverse relationships between C 0 and ripple growth rates and clay winnowing transport rates out of the bed, which reduce as the ripples develop toward equilibrium. For C 0 ≤ 10.6%, higher winnowing rates lead to clay loss, and thus the presence of clean sand, far below the base of equilibrium ripples. This hitherto unquantified "deep-cleaning" of clay does not occur for C 0 > 10.6%, where clay-loss rates are much lower. The clay-loss behavior is associated with two distinct types of equilibrium combined flow ripples: (a) Large asymmetric ripples with dimensions and plan geometries comparable to their clean-sand counterparts for C 0 ≤ 10.6% and (b) small, flat ripples for C 0 > 10.6%. The 10.6% threshold, which may be specific to the experimental conditions, corresponds to a more general 8% threshold found beneath the ripple base, suggesting that clay content here must be <8% for clean-sand-like ripples to develop in sand-clay beds. This ripple-type discontinuity comprises a threefold reduction in ripple height, with notable implications for bed roughness.