A manual transmission uses a driver operated clutch that is controlled by a pedal or lever that monitors torque transfer from the engine to the transmission. Most transmissions make some noise, but if the noise is excessive and does not disappear when the clutch is disengaged, it could indicate a number of problems. There are a few repairs that can help quiet a noisy manual transmission.
Pay attention if there is noise while shifting or driving. This could be due to low gear oil levels, loose bell housing bolts and worn bearings or gears. Replacing fluid to normal levels, tightening the bolts and replacing worn bearings or gears should remedy the problem.
Notice if there is a loud clunking noise while decelerating. This could be due to loose engine mounts, worn inboard joints, or a worn differential pinion shaft. Tightening the engine mounts and replacing the worn joints and pinion shaft should solve the noise problem.
Listen for gear rattling noise while driving. This is most likely due to worn bearings, old or low gear oil and worn gears. Replace the worn bearings, replace or refill gear oil to proper levels and replace worn gears to remedy the noise problem.
Look for gear clash noise while shifting. Worn gears or a broken synchroniser and a faulty clutch is most likely to blame. Replacing the forward gears or broken synchonizers or repairing or replacing the faulty clutch should solve the problem.
Unless you are an experienced mechanic, you should take your vehicle to a mechanic for these repairs if necessary.