The Sethusamudram Canal Project has been at the center of a contention since the time it was first proposed. Various sections of the population have been wary of the proposed construction of a 83 km long canal on the 50 km limestone trail, popularly called Ram Sethu, citing ecological and religious reasons. The building of this canal will require deep sea excavation by dredging and, or blasting the Ram Sethu, resulting in unprecedented ecological disturbance in the area, it is argued. As is the case with most ancient structures, not much is known about the composition of the trail.

Experts suggest that there is inconsistent sedimentation in different parts of the trail and the entire palk bay area, making the ecological repercussions of such large-scale construction on it, impossible to predict. The area is also cyclone prone, with storms in the past having changed sedimentation patterns in the area, further adding to its volatility. There are also fears that such a structure will irrevocably alter the habitat of the vibrant marine life in the area.