They were in love, obviously. Coulson saw it everywhere. He saw it from the start when they would stare at each when they thought no one was looking, till New York when she was so intently focused on him. He could see it their glances, and the way their eyes lit up when they looked at the other. He could see it in the way they were on edge when the other was presumed dead. It was quite obvious.
They cared about each other too much. Fury knew that. He knew it from the start when he wouldn't let anyone touch the girl he was supposed to kill, till the arrow necklace that always hung around her neck. He knew it when Clint wouldn't tell SHIELD about Natasha's past, even though he knew all of it. He knew it when Natasha's goal in the NY battle was saving Clint, and she left a mission when she heard he was in trouble. It would be their downfall.
All of SHIELD knew that Clint Barton and Natasha Romanoff were a couple. Yet they weren't, were they? There was a fine line between lovers and best friends, and they were right on it.
Author's note: Thanks for voting on the poll! As of now, the two top things are Clintasha mermaid au, and Avengers highschool/college au. I'll try to start working on them soon. They will both probably be long one-shots. I haven't started yet though, so if you'd rather me write something else, go vote! Thanks for reading! And sorry for the glitched upload! Hopefully it works this time!