The inter-relationship between the environmental magnetic parameters, geochemical and granulometric distribution are addressed in this paper to assess the environmental conditions employing the surficial sediments of Beypore Estuary, Kerala. The magnetic results elucidate the dominance of magnetic grain size in the lower estuary, magnetic concentration in the middle, and magnetic mineral in the upper estuary, respectively. The magnetic parameters confirm the presence of ferrimagnetic minerals such as magnetite in the estuary. The geochemical elements affinity attribute towards the lower estuary. Further, intense weathering in the lower estuary and moderate to weak weathering in the middle and upper estuary are observed which is reflected in the micro-texture features of quartz grains. The Beypore sediments are moderately polluted based on the pollution indices. The finding elucidates the combination of natural and anthropogenic activities, controlling the environmental conditions in the estuary.