In the present study, environmental magnetic parameters in conjunction with the geochemical, textural, and geochronological (excess Pb-210) proxies are employed to decipher historical changes in the depositional environment of the Beypore estuary along the southwest India. Millennial-scale variations in sedimentation have received many attention of researchers, whereas the centennial-scale changes in sedimentation received comparatively little attention. High sediment loads and high-energy coastal environment can bring significant changes to the estuary. Recognizing centennial to decadal changes of estuarine sedimentation get derelict due to increasing anthropogenic factors. A navel attempt is made here to use the environmental magnetic properties, sediment texture, and geochemistry of the core sediments as proxies to determine the variations in sedimentation for the past three decades vis-à-vis environmental modifications of the Beypore estuary. Abrupt changes in the vertical distribution of constituents corresponds to fluctuations in industrial activities neighboring Beypore area and on the banks of Chaliyar River. Active functioning of the Grasim Rayon’s Factory at Mavoor and its subsequent shutdown in the year 2001 due to public protest have candid reflections in the pollution indicators.