If this is a on demand water heater with a small holding tank, yes you can use vinegar. You will also need a bucket, small pump and a couple hoses. If you are refering to a 40 or 50 gal tank style heater, try flushing it first. Shoule be instructions in owners manuel. Problem is if build up is that bad, when you are done flushing the drain on bottom of tank may not shut off completely due to scale stuck in valve. Without taking pipes apart, how are you going to get vinegar into your tank style heater? Plus it would take a lot of vinegar to descale a 50 gal water heater