This study identified the occurrence of Holocene chronology hiatuses in the sedimentary record of the Patos-Mirim system caused by river avulsion processes, as well as evidence of sharp anthropogenic changes in the surrounding region of the lagoon water bodies. The presence of chronology hiatuses demonstrates the importance of considering the disturbance effect of paleo-drainage processes on the paleoenvironmental resolution and expression of the sedimentary record of such coastal plains. Anthropogenic activities especially those related to agriculture and forestry have increased significantly during the great acceleration, resulting in modifications of both the landscape and the environmental conditions of the lagoon bodies. Such impacts were clearly reflected in the sedimentary record where abrupt changes in palynological trends, sedimentary DNA, isotopic and granulometric analyses were inferred. The climatic conditions combined with regressive sea level can explain the chronology hiatuses. Pollen analyses demonstrated changes in the landscape, particularly indicated by the shift from Cyperaceae to Poaceae dominance after the 1960 CE. Therefore, all proxies together demonstrate the modification in the landscape and changes in the environment, clearly influenced by anthropogenic action from unsustainable agricultural practices. Display omitted •The Patos-Mirim system is extensively dissected by Pleistocene/Holocene incised valleys.•The Holocene record is eroded by currents of meandering streams, which expression consisted of a Middle Holocene hiatus.•Novel palynological and 16S rRNA long-term data demonstrate changes in both landscape and lagoon anthropogenic transformation.