The Barremian–Aptian Morro do Chaves Formation, NE Brazil, was deposited in lacustrine environments during the rifting between the African and South American plates. This formation contains shell beds (coquinas) interbedded with mudstone and sandstone deposits. Shell concentrations may be used to identify paleontological and paleoenvironmental data that allow to interpret the depositional energy, paleoenvironmental conditions and the accumulation history of the formation. The following features of the shell beds were analyzed: (i) taphonomic aspects (sorting, fragmentation, abrasion, rounding and orientation of the shells), (ii) sedimentological aspects (grain packing, abundance of shells, type of matrix and sedimentary structures) and (iii) stratigraphic aspects (bed dimension and shape, bounding surfaces). Two siliciclastic lithofacies (clay mudstones with mud cracks and laminated sandy mudstones) and four carbonate lithofacies (wackestones, packstones, grainstones and rudstones) are described based on the textural features. The carbonate facies were successively divided into six taphofacies (T1 to T6) with the help of an artificial neural Self-Organizing Map (SOM) and evaluated by non-metric multidimensional scaling (NMDS), based on taphonomic features of the carbonate lithofacies. Taphofacies and lithofacies formed at lacustrine margins. Clay mudstone layers with mud cracks and without shells fragments are interpreted as distal parts of alluvial fans or fluvial distributary systems at the edges of the lake system. Rudstones and packstones (taphofacies T1, T2, and T3) with fragmented and oriented shells, wave ripples and horizontal lamination correspond to upper shoreface deposits. Rudstones, packstones and wackestones (taphofacies T4, T5 and T6) that display shells with low signs of fragmentation and abrasion and laminated clay mudstone are interpreted as lower shoreface deposits. A depositional model of the coquinas of the Morro do Chaves Formation is proposed based on the characteristics and distribution of the taphofacies. Moreover, the use of an embedded Markov Chain enabled the relation of the different upper and lower shorefaces in a preferential sequence of deposits of shallowing- and deepening-upward cycles.