The enemy is building land bridges and simultaneously attacking by sea. Is there any way to prevent the enemy from altering the terrain?I mean, disabling some option in the menu or something like that.

Enemy builds sand bridges when they could not path to your base. It happens more often if the enemy don't have flying unit or you have turned off the flying attack group.

The purpose was to let them always have a way to attack you, so it's not optional.

Bridges are basically chokepoints and they are easier to defense than open sea.