The backwaters of Kerala was formed by the combined processes of soil erosion from the uplands during the monsoon rains, the constant beating of the sea – waves on the shoreline, and human interferences in nature's way. The alluvial soil deposits over centuries and millennia filled up the periphery of the sea close to the mountains and hills. It was the result of monsoon rainwater flowing down through thousands of streams, brooks and rivulets on the mountain – sides forming the tributaries of the major rivers draining the vast quantity of monsoon rainwater of 3–4 months each year.

Thus the heavy rains during the monsoons in Kerala eroded the topsoil of the Western Ghats and hundreds of streams and rivers carried the soil down to the seabed for centuries. This soil was deposited in the seashore, which led to the formation of marshes and backwaters along the coastlines especially in Southern Kerala, where width of the land and height of mountains are more than at the tapering ends of the land strip in the south and north.

The seaside under-waves and currents augmented this continuous natural process. Erosion of land as well as elevation of new lands is quite common along the seashores of Kerala. Perhaps tsunamis in prehistoric periods might have changed the topography of the coastal land several times. In historic times, in AD 1341 a great flood in river Periyar, is said to have led to the submergence of old Kodungalloor harbour and the city and to the creation of Vyppin islands at Kochi. Some say that it was the result of an earthquake. That event, for whatever reason, almost reshaped the coastline of central Kerala.

Geological studies have proved that the west coasts are distinctive with varied types of laterite found in the high altitudes as well as below the sea level. Palaeo- environmental investigations in this region indicate a higher sea level about 5 metres higher than present level at several places in coastal Kerala. The regression of the sea some 3000–5000 years ago, must have helped the growth of sand bars that separated the sea from the mainland, and ultimately resulted in the development of the present day coastal landscape and backwaters.

There are several river estuaries (mouths of rivers joining sea) with barrier beaches at several of the 41 west flowing rivers of Kerala.

In the scientific jargon of geologists, "Systematic development of the Kerala coast was the consequence of the transgressive – regressive marine regime, aided by fluvio – marine inter – active process, mainly 10,000 years ago. The transgressive phase 25,000 years ago had seen the sea waters lapping at the foot hills of the lateritic cliffs."

Such interventions by the Arabian Sea had a role in the shaping of the geography of the Kerala coastal plains and the backwaters.

The elevation of the terrain of Kerala from Arabian Sea might have been caused by some natural calamities like earthquake or by simple withdrawal of the sea.

The geological surveys and oceanographic excavations carried out in the coastal belt of Kerala give indications about the genesis of Kerala. Centuries ago, the Arabian Sea waves embraced the feet of the Western Ghats and sea shores stretched from the valleys of the hills. Place names like Kaduthuruthi, Kadapra, Vyppin, Vaikom, Thrukkakara, Thruppunithura, etc. bear testimony to the fact that the shoreline was much interior at one time.