Recent studies have unearthed and recovered multiple sites with evidences of past human habitations in terms of ceramic, metal, precious stone, jewel, and stone tool industries and places of varied methods of burial and worship are being unearthed at different stratigraphic levels from floodplains of the Vaigai River Basin, Southern India. In this contribution, we present high-resolution 14C chronology of the archaeological artefacts, cultural evidence and the textural characteristics of sediments collected from the excavated pits. These data along with the information on regional geology, geomorphology, sedimentary facies, texture, petrography, and mineralogy constrain the older phase of the Vaigai River Basin Civilization to be microlithic in age, followed by affirmative evidence of ca. 5511-5147 BCE (7455-7091 cal yr BP). This was followed by few more colonization/cultural/habitation sites/surfaces at ca. 2976-2961 BCE (4938-4908 cal yr BP), 1860-1489 BCE (3543-3503 cal yr BP),530-390 BCE (2435-2314 cal yr BP), 596-629 CE (1353-1321 cal yr BP) and post 1225-1312 CE (729-619 cal yr BP). These are designated as habitation sites/surfaces namely HS-1, HS-2, HS-3, HS-4, HS-5 and HS-6, respectively. Evidences of urbanism, industrial and leisure activities besides cohabitation of at least three groups that practiced mutually exclusive burial customs are documented. Microlithic tools and buried habitation stages, together with the prevalence of modern habitations, make this basin unique with human occupation at least since the mid-Holocene. Major shifts of the trunk channel of the Vaigai River, perhaps associated with flood events, marooned/buried/destroyed the ancient habitation sites that forced the inhabitants to abandon old sites and led to the reestablishment of newer ones. Inevitable dependence of the ancient societies on the riverbanks and the flood plains for settlements and livelihood compounded with the lack of knowledge on extreme climatic events possibly caused the decimation of several settlements of this important civilization from south India. © 2021 The Author(s)