The south-west depression of Kerala-Konkan onshore peatland is one of the most promising areas for shallow biogenic methane existence in India. The shallow biogenic methane gas in the area is intimately linked to the sedimentary environments and palaeo-drainage system emerged due to the evolution of the West coastal system as the result of sea level fluctuations. Depressions caused by such fluvial incisions were drowned and filled up by sediments during a subsequent transgression in the study sites. The main purpose of this study is to identify the spatial distribution of hotspots by surface-based non-invasive GPR surveys as the tool for estimating free phase gas fractional volume from multi-offset profiles by using Complex Refractive Index Model (CRIM). The peat layers of Holocene–Pleistocene age in the sub-coastal areas of Southern Kerala Sedimentary Basin (SKSB) were mapped with ground-penetrating radar (GPR) with frequencies of 100MHz. The formation of biogenic gas from the peat is either by acetate fermentation pathway or CO2 reduction pathway and is accumulated as the by-product of anaerobic decomposition of organic materials. The escape biogenic methane encountered at the depth of 3–4m and 16–18m on the coastal inland area few kilometre far from the present coastline. Cross-sectional plots display the spatial variation of gas dynamics identified based on the shadow zone due to the variations in electromagnetic wave velocity and amplitude of radar signals have significant correlation with direct measurement of free phase gas (FPG) volume. A conceptual model developed from the present study based on the escape or loss of methane from peatlands via two mechanisms—one, by shallow diffusion and episodic ebullition (from 3 to 5m depth) of methane from the peat pores matrix and second is, the deep ebullition (from >16m depth) processes due to the breakage of confining woody peat layer, which causes a large rates of abrupt escape of methane from peatlands to the atmosphere evidenced by the GPR measurements. © Springer Nature Singapore Pte Ltd. 2019.