Why does it happen?

A ship dips to a larger depth in fresh water as compared to marine water.

Density of fresh water is lower than that of fresh water. This is due to the very lower concentration of salt in fresh water. Buoyant force on an object is proportional to the density of liquid. More the buoyant force, object can easily dips to larger depth. So a ship in fresh water experience higher buoyant force than that in salt water. So it dips into larger depth in fresh water than in fresh water.