This may be similar to or ever the same as this issue, but I wanted to provide some further clarification/additional reasons why this should be investigated. I know it's entirely possible that the complex nature of world gen may make it not fully resolvable, but I'm optimistic! I am currently playing TerraFirmaGreg, using their latest release that appears to be using TFC version 3.2.2 (their change logs haven't stated any later version being used since their version 0.7.3, and they are currently releasing 0.10.9), and they sent me over here from their repository stating that this was an issue that stems from their usage of TFC.

The attached images are from the same river structure in a world I created in TFG (I can provide the seed, but I'm unsure if it will produce the same worldgen thanks to the TFG team's extra modifications beyond TFC). The river is flowing adjacent to and through an Oceanic Mountains biome that seems to be pulling in sea water further inland due to biome weights/generation. The problem is that it interrupts the flowing water generation and it seems sea water is generated after normal water. As you can see in the images, some of the underground river maintains its flowing quality, but anywhere there is an abrupt start or stop it is because of sea water that seems to be generating due to the surrounding Oceanic Mountains biomes regardless of whether the F3 menu states the water is in a River biome.

I'm wondering if it is possible to allow sea water to be set to flow like normal water, or if it's possible to force sea water generation to occur prior to normal water specifically in River biomes.

Hi, unfortunately this isn’t something we’d change in 1.20 this far along, and is more or less a design choice we made when making the mod. We can revisit for 1.21