Coquinas are important carbonate oil reservoirs in the sin-rift sequence of the Brazilian marginal basins, mainly in Campos and Santos basins. They are generated from shell accumulations in lake-margin environments in which waves and bottom currents, at storm conditions, were the main hydrodynamic agents of transport and reworking. In order to investigate the role of wave transformation processes in shallow waters – swash, breaking and wave shoaling – in shell concentrations, a physical modelling of the coastal environment was performed in laboratory. The experimental setup consisted of a 2D flume, a wave generator, and a sedimentary bottom composed by quartz sand and shells (bivalves, gastropods, and fragments). An underwater camera, wave gauges and an ADV were used to record the sedimentary processes and to perform a quantitative analysis of the hydrodynamics. The experimental scenario reproduced a rift-lake margin. A coastal sector of Lake Tanganyika, Tanzania, Africa, was used to set the model boundary conditions (in a 1/20 scale) as well as the coastal gradient and wave conditions. From 54 h of wave experiments which alternated from fair-weather to storm wave conditions, three shell concentration dynamics were observed: reworking, winnowing, and dynamic bypassing. The reworking (erosion) was characterized by traction, rolling, and saltation of bioclasts, together with the traction and suspension of sand. The occurrence of the latter was restricted to the breaking and swash zone in both fair-weather and storm conditions. The winnowing (erosion) was featured by sand suspension and the gentle traction and rotation of the bioclasts on the bottom. The winnowing occurred at the proximal area of the shoaling zone, just behind the first wave-breaking point in storm wave conditions. The dynamic bypassing (omission) was identified by the ripples migration over static shells on the bottom of the distal shoaling zone, which produced alternated burial and exhumation of bioclasts. The quantitative analysis of the oscillatory flow indicated higher velocities at the breaking zone (reworking domain) than at the shoaling zone (winnowing domain) mainly during storm conditions. This study provided new and more accurate insights to depositional models of lake-margin coquinas, suggesting that each wave transformation process control a specific dynamic of shell concentration. Also, the limit between the breaking zone and the shoaling zone in storm conditions (1st wave-breaking point), was identified as a better criterion to bound the reworking domain, where fragmented coquinas are produced, from the winnowing and dynamic bypassing domains, where non-fragmented coquinas occur, in contrast to the fair-weather wave base criterion.