A lot of changes occur in the 400 year difference between the Past and Present, including the subsiding of the sea. This can be seen by the larger land area of Crescent Island, along with the expansion southward of the South Shore. Additionally the Sea of No Return, previously an area at the east end of the overworld that was surrounded by water, has now become connected to much of the land and is now the location of the Yoll Graveyard. Previously where Ambi's Palace was located is now the location of the Nuun Highlands.
Throughout his quest, Link will travel to the Past and can move vine plants around. When traveling to the present, this can cause large vines to have grown on walls.