Although I am sure that washing produces a better quality Biodiesel, there is still some controversy over its necessity.  The alternative is to allow the glycerin and soap and other impurities to settle out with time.  I spent the first couple years of my homebrewing journey just letting the Biodiesel sit for three weeks before filtering and using it in my car.  Although it “worked” well in my car, I did see some accumulation of glycerin in the bottom of my fuel filter, which of course means that glycerin was settling out in my fuel tank and perhaps other places.  Also, soap and salt and other impurities are certainly not good for ones engine.  So, although it takes more time, I have joined the ranks of the washed. 

It is important to allow your biodiesel to sit for a few days (3 days recommended) before even starting to wash. This allows enough of the soap and glycerin to settle out so you won't have emulsification problems when you start washing. If you don't wait those 3 days, you may get mayonaisse when you start washing!

My wash procedure involves using rainwater and the bubblewash method.  I fill carboys with rainwater, and add 30 ml of vinegar for each 100 liters of Biodiesel I’m washing (according to Mike Pelly’s method) for the first couple of washes.  This helps bring the pH down to neutral and also helps prevent emulsification with any soap present in your Biodiesel.  Soap is formed as a byproduct of making Biodiesel (see Figure 3 from Mike Pelly’s description). 

Optimally one should use a ratio of water to Biodiesel of about 1:3.
I don’t have room in my wash tank for that much water, so my ratio is about 1:4, which causes me to have to do more water changes. 

As shown above, I set the water carboys on a shelf even with the top of my settling/wash tank, and then siphon the water to the bottom of the tank.  You want to add the water gently again to avoid emulsification (see troubleshooting).   I am now using an aquarium bubbler which can be adjusted for the amount of air output; this is very important, because during the first couple of washes, the bubbling should be very low.  Then you can crank it up a bit!  I use the Million Air pump and wooden bubbler from Utah Biodiesel Supply both of which work great.  It is also recommended to heat the wash water a bit which speeds the process (and is essential in cold weather).  For this purpose, I use a 350 W titanium aquarium heater (available from Utah Biodiesel Supply, or from many sources on eBay) which keeps the 60 gallons of liquid at 80 – 90 degrees F. 

The first wash should be fairly short- I keep mine to an hour or so with very gentle bubbling.  Drain out a cup of the wash water- if it is very cloudy, it is time to change it.  Subsequent washes can be several hours to overnight.  Continue doing water changes until both the wash water and your Biodiesel are clear (or very nearly clear). 

Sometimes it is difficult to get the Biodiesel completely clear.  Many people have found that simply bubbling air through the Biodiesel can clear it up though no one seems to know why it works.  I think it is important to let the Biodiesel sit for several hours to overnight after washing, to allow any water to fall out.  It may seem paradoxical, but, the better washed the Biodiesel is, the less water it will hold, because there will be less soap for the water to stick to. 

I dispose of my wash water down the toilet.  My rationale here is that it is a lot better to send the wash water to the sewage treatment plant than to pour it on the ground where it could get into streams and lakes.  The wash water contains enough methanol that it could kill plants and other organisms. 

Note that there is a section on drying Biodiesel on the Biodiesel Community website. Drying is important, because the washed biodiesel will hold onto some water and will appear hazy, especially after cooling down (if you've been applying heat during wash).  I prefer the method of simply bubbling air through the washed biodiesel overnight. That clears it the haze beautifully!

Note 2: Some folks do a "dry wash" using either Magnesol, which is magnesium silicate, or amberlite, which is a resin. Magnesol is a very fine powder and is hard to filter out, but check out this setup for a way to make it work (using a spinner filter). Still looking for homebrew tests with Amberlite- let me know if you've tried it! (try searching infopop for some experiments).