We live in a place where "damp" is at its best. Nine months of the year we are damp, our city is damp, most of existence outside is just plain damp. You can smell the rain coming around this time of year and then it just doesn't leave. In my opinion, it is part of what makes here so wonderful - Drippy, soggy, unending rain.
This is also the reason our rain barrels are so well suited to our house. They just don't go dry. We can flush toilets, we can do dishes, I might even begin washing laundry and they don't go dry. Dry just doesn't happen in our rainy season.
This constant cycling of water, is one of the main benefits of cleaning our rain barrels. The barrels need to be cleaned yearly, even if you only use them for irrigation. This is due to the algae blooms which will occur. There is nothing harmful about this algae, in fact it probably makes the water much nicer for the plants, but it can clog the spigots and make using the water difficult. Some people use fish or snails as a way to remove the algae which builds up inside. It seems to work for them, but I have no experience here. We use standard Clorox.
Two to three months of the year there is NO rain. It is as though the rain goes on summer vacation too. So, in late summer, as late as responsibly possible, we begin once again using our rain barrels for much of the household water. The barrels are at their lowest, and we begin to quite rapidly drain them for dish washing and toilet flushing.
I add 1/2 cup of bleach to each full barrel. This means that as the bleach dilutes in the water, it is able to kill any of the algae clinging to the walls. The barrel sits for 24 hours to make sure the bleach has really permeated and then the barrel is drained with usage. DO NOT USE THE WATER FOR IRRIGATION at this point. It will kill your plants. It will kill any wonderful mycorrhizal fungi at work in your soils. The point of the bleach is to sterilize and it will sterilize anything the water goes near. This makes such water ideal for dishes and toilets. The first 2/3s of the barrel I use solely for dishes, the bottom 1/3 starts to get a little ookier with dead algae and sediment. Such things need to come out of your barrels, but don't necessarily need to be in your dishwater. This last 1/3 goes to just toilet flushing. The bleach water is excellent for the toilet tank and pipes, and the residue in the water doesn't matter.
If your rain barrel is a solitary barrel (not attached to a system or other barrels, just by itself) you can use a wrench to take off the spigot, disconnect it from the downspout, and tip the barrel toward you to allow every last bit of water out (a 30 degree angle works best). You can then spray out the barrel with a hose if need be and leave it to sit in the sun for 48 hours. This will completely sterilize the barrel and you are good to go for another year.
However, only three of our barrels are solitary. They are our just-in-case, backup barrels. The main ones we use are all hooked together and do not tip at all. These barrels will always have at least 6 inches of water in the bottom of them. There is no way, other than completely cutting them free, that they tip and can be totally drained and rinsed. For this reason, we clean them a bit differently.
We begin draining at the last in line (Barrel 5) and take as much water out as possible. I work backwards (Barrel 4, 3, 2) bleaching and draining all the way through. I never bleach Barrel 1 which is hooked to the downspout. (This means at least one barrel at all times has fresh rain water.) At the point all but Barrel 1 are drained there is still 6 inches of bleach water sitting in the bottom of each barrel. When the rains come this water is diluted as the barrel fills and cycled through the entire system. All the overflow bridges get bleached, the main overflow gets bleached, and the entire system is cleaned. Slowly, but surely the bleach water is dissipated through out the barrels and in a month, there is no trace of bleach.
Six inches of slightly bleached water diluted in a 55 gallon drum is not a toxic level. You can still smell it, I don't really want the dog to drink it, or to irrigate with it, but it won't hurt much that is very large. As the water goes through the pipes of the toilet, or sanitizes the dishes in our sink, the cleaning works double duty in our house. It takes only two weeks to completely drain all 9 of our rain barrels, and a month for the entire process to cycle through the barrels. In my opinion is is very low maintenance for the return.
I have heard there are fancy chemicals you can use, weird tools you can acquire, or various organisms which people use to do their cleaning (and maybe we will one day get there) but for right now, we will stick to our $2.50 jug of bleach and our unending rain.
Other Helpful Resources
Approved Bleach for Sanitation of Drinking Water
The University of Texas has done significant research into varieties of bleach. Apparently, all bleach is not created equal. (Who knew?!?) If you are using your rain barrels for drinking or to create potable water, be sure to check this site out!
Storing Water for Emergency Use
Colorado is currently facing quite a water crisis. For this reason their agricultural extension has a wealth of information about storing water. Included is information about amounts to store, ways to sanitize, and different storage techniques.
Preventing Food/Water Borne Injury and Illness
As I began looking for information on safely treating water for household use, I kept getting websites or books about sailing on boats. It was frustrating and made no sense to me. Then I realized (with Jules' explanation) this is because when doing long distance boat travels, sanitizing water, storing sanitized water, and learning how to utilize treated water are imperative skills. Sometimes valuable information is found in the oddest of places. This is one of the absolute best places I have found for information about sanitizing and using water. The writers not only do a lot of long distance boating and have used the methods, but are medical professionals (ER doctor and pharmacologist; registered nurse and paramedic).