You won’t find recommendations or articles from health authorities about sanitizing plumbing or drinking water equipment with vinegar because it isn’t very effective. Some bacteria and fungi like an acid pH, which is obvious since they are used to make vinegar. A moderately low pH may inhibit their activity, but it won’t kill them and as soon as the pH becomes more pleasant for them, they leap back to life.
The same goes with baking soda; a pH of greater than 10 is required for effective sanitizing and will kill all microorganisms, but baking soda solutions have a pH of 8.4 or less. Like vinegar, it will reduce their numbers, but not dramatically. But this does not mean that vinegar, citric acid and other acid cleaners do not have a place in restoring neglected potable water systems.
We’ve recommended borax-based formulations for killing and preventing the return of mildew. Some of the effectiveness derives from high pH (mildew prefers low pH) and some from its natural antibiotic activity. But borax is too toxic to use around drinking water, so scratch it off your list. It is safe for surface cleaning, fabric treatment, and skin contact, but it is forbidden in potable water systems.
Hydrogen peroxide and peracetic acid are effective sanitizing agents, often used in food processing industries, but they are highly toxic and must be thoroughly rinsed from the system prior to use. We think they are too hazardous for DIY use at the required concentrations without training.
We have recommended bleach for sanitizing potable water systems—it is the ANSI-recommended method. But it is not effective on plumbing with significant scale or biofilm build-up, because no sanitizing agent can quickly penetrate thick deposits. For this, a good acid cleaning can help.
We’ve studied many acid cleaners for their ability to remove scale, dirt, and oxidation from metals and hoses. Muratic acid, lactic acid, and phosphoric acid are highly effective, but we would rather not use these in potable water systems, because of safety issues and the risk of damaging susceptible metals. Vinegar and citric acid are two traditional choices for cleaning potable water systems, both in RVs, boats, hospitals, and in poultry watering systems. After as 3-6 hour soak, a 1-3% acid concentration will kill more than 85% of giardia cysts, and after 24 hours they will kill over 98%, something bleach cannot claim. The acidity dissolves their protective coat and the scale and biomass layers they are hiding under.
Don’t mix any acid with bleach, in the mistaken belief this will be a one-step miracle. The acid will cause the rapid release dangerous amounts of chlorine gas. If you chose to follow acid cleaning with bleach sanitation (probably not needed) be certain to rinse the plumbing with copious tap water to a neutral pH before adding bleach.
White vinegar is certainly the more available, but we’re recommending you give citric acid a try. It is a more effective descaling agent, in part because it is a double acid, and it has many uses around the boat (see “Passivating Stainless on Sails and Gear,” PS March 2022). It removes scale with less damage to underlying metals, you avoid the stink, and it is cheaper.
We’re not saying you need to acid wash your plumbing. If it has been well maintained, probably not. But a new-to-you boat that has been neglected, or if bleach sanitizing has not resulted in fresh water, an overnight soaking in vinegar or 3-5% citric acid could do the trick.