The Sea (the first body of water in the Legacy of Kain series not to be named as a "lake") is first seen to border much of Southern and Western Nosgoth in the opening video to Blood Omen 2 later Kain would travel along the edge of the sea to reach the Eternal Prison and even catch a ship from the Wharves to reach The Hylden City and Hylden Gate on an island chain across the sea[BO2].
Although not identified as such; the waters seen in The Canyons, the Slums, the Smuggler's Den, the Wharves and The Eternal Prison likely flowed to, or were part of the sea. The Hylden City and Hylden Gate were both surrounded by it and the town of Freeport was also situated on its coast[BO2].
The Great Southern Sea is only seen in a map, in the dream sequence of Blood Omen 2 . It is not explicitly identified as such in levels, but given Meridian's coastal location it is likely much of the water in Blood Omen 2 is somehow connected[BO2].