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I don't have any plants established in my newly made system yet but what are some good guidelines as to how much airtime roots should have between floodings? I'm using a window box liner set on top of a 10 gallon fish tank and it fills up pretty quickly so if I need to I can use a timer on the pump to help regulate the amount of airtime plant roots get.

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As long as the water is well aerated and your circulating enough water through the bed to keep it well aerated, the plant roots don't necessarily NEED any air time.

So if you are using a siphon, just use what ever timing it balances out at, anything else will just be a struggle.

If you have a timer, you will use whatever increment per hour it gives you, like if it has 15 minute increments, you will probably set it for 15 on and either 15, 30 or 45 off.  If it is a timer with only 30 minute increments you will set it for 30 on 30 off.  If it's a digital timer you may have an issue since they usually only give you a limited number of on/off cycles per day and it usually would only work out to between 7-14 on cycles per day so you will be stuck with not enough cycles per day to flood hourly and you will have to make something up.

There are some systems out there though that don't even bother with air time and they just run constant flood.  Some plants like this better than others and it will vary depending on the situation.  If you can keep the top inch of media dry most plants do ok with it though.  If the top of the media stays wet, it can be more problematic and watercress will be a good choice of plant.

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