Flushing and Sanitizing Your Water System

Flushing the Lines 

On the initial hookup of the water supply to a newly installed piping system, all the lines should be thoroughly flushed to remove any particles of dirt or debris that may have fallen inside the pipe lines during assembly.  If the lines are not flushed, then these particles will be carried into the drinking valve, where they may become lodged on the seal and cause a leak.
To flush the line, open the drain valve at the end of the line and allow the water to flow out for several minutes.  Repeat this procedure for each drain valve in your system.  Start on the lines that are closest to the water supply and work your way to those farthest away.  Next flush every line going to the valves.  Remove the valve from the end of the line and flush.  Start on the valve closest to the water supply.

Sanitizing the Plumbing System

For household potable water systems it is a good plumbing practice to sanitize the lines on start-up to eliminate bacteria in the pipelines.  This is also a good practice to follow for your Automated Watering System.  Sanitization of the lines can be easily done by filling them with a chlorine solution and allowing them to stand for at least 30 minutes.  It is recommended that the chlorine solution have a concentration of 5 to 10 parts per million (ppm).  This will not harm the animals/birds if they should drink it. 
You can easily prepare a chlorine solution by mixing household chlorine bleach and water.  A solution of ½ teaspoon per 7 gallons water will produce a solution of approximately 5ppm.
The method of filling your pipelines with the sanitizing solution will depend on the water supply method you are using.  If a Storage Tank is used, you can fill it directly with the sanitizing solution.  If a Float Tank is used, the fresh water supply must be shut off and then the tank must be filled with the solution.
Once you have sanitizing solution as your water supply, you should flush each line (including the line going to the valve) just long enough to fill it with the solution.  Then allow the system to sit for at least 30 minutes before flushing the lines with fresh water.

Doing this once a month is advised.