A dataset of 176 channel bed sediment samples allows a detailed analysis of mud pebbles (defined as mud clasts ranging in size from 2 to 64 mm) forming along the fluvial to marine transition zone (FMTZ) of the Mekong River delta. These mud pebbles are typically up to 4 cm in size, spheroidal to subspherical in shape, well rounded, and well sorted; they are associated with a sand matrix and can make up more than 50% of the sediment volume. The mud pebbles were found in ∼ 52% of the collected samples, along the more than 200-km-long studied distributary channel and in both dry and wet seasons. They formed as relatively high-energy currents eroding previously deposited fluvial and tidal mud layers. The spatial-temporal distribution of mud pebbles suggests that they were produced by fluvial currents with subordinate tidal influence during the wet season, and by tidal currents with little or no fluvial influence during the dry season. The observations of this study provide new criteria to identify in-channel FMTZ mud pebbles, differentiate them from other types of mud clasts, and use them as a tool to constrain sedimentary processes in modern and ancient FMTZs.