While there is no hard and fast ‘rule’ that says you must do it in a particular way, but most growers generally allow their air pumps to run for 24 hours a day, particularly if their plants have their roots which are deep inside the reservoir. Using air pumps all day will also ensure that your plants remain safe from algae or other water-borne pathogens. This also reduces the stress on the roots and ensures that your plants grow healthier and have stronger roots. However, if you wish to do so, you can turn off the pump every now and then for a short duration.