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This is a key part of your system, to keep everything running smoothly. Timers are important for lights as well as the water system. Lights just need to go on and off each day, but you will be running a pump several times each day (and through the night too).
Simple household timers are not going to be suitable for your water pumping arrangement because they usually don't allow for enough on/off cycles in a day. There is no specific right or wrong way to cycle your water system, so only general guidelines can be given here.
It will depend on your style (deep water vs. ebb/flow) and the type of medium you are using. As we mentioned in the section on growing materials, one that doesn't hold water will dry out much faster than a porous one that soaks it up. That is the kind of thing that impacts your timing. A common pattern is that your grow beds are flooded for 15 minutes, drained and then again in 45 minutes. You may need to run it more often if the roots are drying out before the water comes back through. Two cycles per hour is usually sufficient.
That means you have to have a timer that can handle approximately 24 on/off cycles each day. Some better quality household timers can manage that, but an aquaponics supplier may have better options for you. Plan for around $100 for a good timer. Of course, if you are running multiple grow beds with several pumps, each one will need its own timer.
You can use the same cycling pattern for a deep water tank though you can run your pumps a little less often since your aren't leaving your plant roots high and dry during the process at all.
Now, all this talk about timers implies that you are doing a flood and drain cycle with periods of no water movement in between. While this is the most common approach, you can eliminate the timing completely and have the water flowing constantly. It does simplify things but you run the risk of oversaturating your plant roots or even stressing your fish due to excessive water movement. It can certainly work once you have a bit more experience under your belt though. Something to keep in mind.
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