Trailing arm bushings can crack and break resulting in a clunking or rattle noise over bumps. Cracked bushings will require replacement.
Problems for specific Honda Civic years:
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Most reported 1999 Honda Civic problems
On certain models the upper windshield molding vibrates at a higher speed causing a noise. Back filling the molding with silicone sealer will eliminate the noise.
The AC idler pulley can fail causing a growling noise from the engine. A new idler pulley will be needed.