Shell midden formation is largely controlled by anthropogenic processes, resulting from human exploitation of aquatic resources. This makes shell middens archives of both human behaviour and palaeoenvironmental records. However, their often complex stratigraphy hampers the isolation of individual anthropogenic events. In the central/ southern coast of Portugal, extensive inland estuaries were preferential settings for Mesolithic groups from c. 6200 cal BC. Here, we present a microstratigraphic approach to the shell midden of Poças de São Bento, one of the largest and best-known sites in the Sado Valley. The microfacies approach was based on sedimentary components, their abundance and arrangement, and post-depositional processes. Anthropogenic processes identified as tossing events and anthropogenically reworked deposits allowed inferences on spatial organisation, preferential refuse areas, occupational surfaces, and temporality of the occupations. The presence of calcareous pebbles in the anthropogenic, shell-rich sediments, together with foraminifera, presumably from the estuarine marshes, is compared with the regional geology, providing a hypothetical location of the shellfish gathering. The microstratigraphy described reveals a full internal dynamic in the formation of the apparently homogeneous shell midden layer. The human activities inferred at Poças de São Bento have many similarities with those reported for Cabeço da Amoreira in the nearby Tagus palaeoestuary. This evidence points to the need for further micromorphological approaches in similar deposits. The study of shell midden formation processes, through integrative microcontextual approaches, plays a major role in understanding Mesolithic societies in the large early Holocene estuary environments of Atlantic Iberia.