There are different chemical elements present in sea water and freshwater rivers and ponds that make them distinguishable by laboratory tests. For instance, it is possible to tell the difference between some freshwater growing areas. With Japanese pearls grown from lake Kasumigaura and the look-alikes grown in China - one has more gallium and one has more barium, and they have different levels of strontium. Probably more information that you ever wanted to know, but it is possible to tell them apart forensically.