If you're just changing the hero's sprite into the 'boat' sprite, you'll need to make a new tileset type just for that map, that has the water set as 'passable'.

Basically, go into the database, Tileset tab, increase the array size by one, copy the tileset you're using into the new slot, and change the water's passability to 'O'. Then change the map's tileset (in Map Properties) to your new one.