This research attempts to provide a contribution to the study on coastal barrier‐lagoons in the SE Africa generated by sea‐level fluctuations, and climate change during the Late Holocene. To achieve this goal, the grain‐size analysis and morphoscopic description helped to detect cyclic facie sequences with sediments sized over 200 μm mixed with silt, bioclasts and organic matter. Moreover, the magnetic susceptibility and X‐ray diffraction (XRD) analyses displayed over 90% of quartz and isolated mica, feldspar and heavy minerals. Additionally, the X‐ray fluorescence (XRF) results display the interplay between terrigenous (>Ti and Al) and marine influence (S, Cl and ~Ca) over the last ~3,500 cal. yrs. BP. The geochemical tracer fluctuations detected suggest five distinct deposits including beach, washover, lacustrine system, aeolian deflation that rest on top of the Pleistocene palaeodunes, which are tentatively associated with the sea‐level variations, extreme marine events or with local floods. Although the multiproxy data record refers to a study in Bilene‐Mozambique, it is interesting to understand the mechanisms and variables related to the evolutionary dynamics of coastal barrier lagoons generated by sea‐level fluctuations and climate change, especially in the SE Africa.