I am trying to fill in a large area of water using baritone but it seems to get confused and just sinks me to the bottom. Is there anything I can do to make it fill in the water?

ive tried using sel cleararea and sel fill , but neither work

#sel cleararea is effectively the same as #sel fill air so that's to be expected.
The problem with what you want to do is that Baritone can only swim on the surface so there is no way for it to reach the positions where it has to place the block. The reason it sinks down is that it defaults to not doing anything at all, which is a bit questionable when in water.
If you want to get rid of the water you could try replacing the top layer with solid blocks, then removing those and replacing the next layer until all water is removed.