The gargantuan can’t live in the lost river, it probably died from old age and it carcis was shifted into the lost river from tectonic shifting.

Im just wondering what if the lost river was a breeding ground for them when it was more open and then the gargantuans that died there supplied so much nutriens that plants and other life form's started appearing

Maybe it was swimming over the lost river, and Kharaa killed it

Leviathans can’t die to kharaa

The Most Logical Explanation Is That While Wandering Around The Lost River The Gargantuan Leviathan Was Attacked & Killed By Either Ghost Leviathans, River Prowlers, Or Even Sea Dragon Leviathans.