Hi. I have a 99 Honda Civic LX with manual transmission. When the weather it's cold and the car is outside overnight, I am having a problem putting the transmission in any gear when the engine is running with the clutch pedal pushed all the way to the floor. I also noticed that the clutch pedal is spongy when I press it. I checked the clutch fluid reservoir under the hood and it was empty so I filled it up but I am still having the issue with not being able to place the transmission in any gear in the morning and the spongy clutch pedal. I checked the hoses for any leaks but there were none visible. If I pump clutch for a couple of times in the morning then I am able to put it in gear. What can be causing this problem?

 

Faulty Clutch Master and/or slave cylinders. diagnose per factory service manual and replace as necessary.

it also wouldnt hurt to adjust pedal free play after the repair is done.

If after you fix the problem, the pedal is still spongy or you still have trouble putting it into gear, look into the clutch fork being bent/warped. Past that, your pressure plate may have issues. But, having said spongy, I would look to the cylinders first as you said there werent any leaks from the pipes/hoses.