Many ancient settings differ from Holocene shallow seas, and studies on quantitative taphonomy carried out in modern shell beds do not necessarily answer all questions that the fossil record may raise. In order to help characterize past environments, sedimentological shell beds from a Lower Pleistocene fan-delta system are analyzed. The studied sandstone intervals, cyclically alternated with a mudstone facies, were deposited in a tectonically active setting during phases of advance of fan deltas. High-density flows triggered by river floods mixed skeletal remains from different shallow-water communities. Standardized quantitative taphonomic procedures tested in modern settings are applied for the first time to fossil bivalves. The study shows that intrinsic factors did not overprint the pattern dictated by extrinsic agents. Damage levels are inversely related to sedimentation rate and directly related to the volume of high-density flows, although the influence of other agents cannot be eliminated. The most revealing taphonomic variables are fine-scale alteration, edge modification, fragmentation, and discoloration, while bioerosion and encrustation were insignificant, due to generally high rates of sedimentation. The study suggests different sources of skeletal remains. Fine-scale alteration, edge modification, and fragmentation are higher in shells from aerobic muddy sediments, and it is suggested that these remains came from erosion of older, tectonically exposed sediments of the mudstone biofacies. The majority of shells are fresh and came from nearshore sandy and muddy biofacies. These are interpreted as contemporary, or nearly so, to the depositional events. The overall results underline the importance of active tectonics in causing repeated burial/exhumation cycles and episodic burial of articulated, or otherwise pristine, skeletal remains, causing the frequent mixing of taphonomic signatures through lateral transport. This situation may be characteristic of other fan-delta systems from ancient structurally confined basins.