Flotsam are loot boxes you can find floating in the ocean, they can have varying degrees of rarity and always contain some gold, at least one blueprints and food item, usually a song, and sometimes also resources or other items.
They can be seen as floating, rotting wooden crates covered with barnacles and seaweed and have a glow around them, indicating Item Rarity.
You can recover the items either by swimming up to them and pressing e to open, or using the 
Grappling Hook to haul them into contact with the vessel.