you can say on pond tiles that they are part of a multi-tile object with a reference to where the actual data is stored
if there is no data then you can create a type for each sub tile of the large object and just store those, so you can find the orientation and bounds by just looking at the type
in game you can have it act as one object.
edit: let say your pond is a 2*2 and needs no other data, then you create 4 tile types pond0, pond1, pond2, pond3, with pond0 the top left file. when you place a pond then you check if all tiles are free and then change all the tiles into the appropriate pond tile
when you interact with it then you forward the interaction to all tiles of the pond and have them act on it properly, (start glowing; have one trigger a sound, etc.)