I can clearly hear a sort of wine when it push the clutch in. It started after I drove through about 1.5-2ft of muddy water. I was in the water for for about 20min. due to the fact I was kind of stuck Is the noise anything to be worried about?

 

So your transmission was submerged in muddy water?

Make sure its not just the pivot fork on the outside of the transmission that is squeaking.

Might be time for a clutch job..

 

I had the same problem a couple months ago, when I changed the clutch it was fine

 

probably the throwout bearing. there isnt anything protecting it inside the bellhousing. only thing to keep crap out is the boot around the pivot fork. could pull that boot off and put some water in there and see if it comes out the bottom muddy. if it does you probably have a considerable amount of crud in there that could be causing that sound.

 

I had a problem with that seal. It had rusted the pivot that the fork rides on. So I got a VERY anoying chirping sound.

Greased it then used clear silicone to seal the rubber boot to the tranny, never had an issue after that.