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.
Problems for specific Honda Civic years:
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Most reported 1999 Honda Civic problems
The evaporative emission control solenoid can fail in areas of the country where salt is used on the roads during winter. The solenoid needs to be replaced to correct this issue.
Trailing arm bushings can crack and break resulting in a clunking or rattle noise over bumps. Cracked bushings will require replacement.
Some models have an issue were the windshield wipers won't shut off due to a bad internal switch. The wiper motor needs replacing for this issue.