Environmentalists fear that there are two ways in which the plying of ships could endanger the ecology. Dredged spoil dumped in the vicinity of the islands could cause mass, suspended sedimentation. The canal would cause a change in the magnitude and direction of currents in the Gulf of Mannar because it will be 300 metres wide, and the changed currents will flow towards the 21 islands.

Sethusamudram project will also adversely affect the Palk Strait between India and Ceylon which is about 75km-wide, with a water depth of 9-13 m, except where local coral reefs rise above the sea level. The Palk Strait is an inlet of the Bay of Bengal. The Palk Strait is 64 km to 137 km wide and 137 km long. The Palk Bay is also considered as one of the five major reef formations in India1. A total of 61 species of algae are distributed among the three major groups and diverse seagrass meadows in the country.

Gulf of Mannar Biosphere Reserve is one of the world's richest regions from a marine biodiversity perspective. The Reserve harbours marine biodiversity of global significance and is renowned for its coral reef, sea grass and algal communities

A busy continuous navigation in this region will offset and trigger devastating ecological imbalance, affecting the lives of millions of fishermen and many endangered organisms of the subtropical, shallow Gulf of Mannar.

This whole SSCP area is a biologically rich and rated among the highly productive sea of the World. The SSCP could cause huge impact to the Ocean Ecosystem Says Manitham Report

Turtle lovers and marine scientists have raised objections to the project, fearing it would change the migratory path of Olive Ridley sea turtles towards the Orissa coast and endanger their lives.