How long the pump runs on start up depends on the age of the controller, from 2002-2011 it was 20 seconds. From 2011-present it is 15 seconds. This is needed to prime the pump and start up and verify function while you are their setting it up, that is why this feature exists. It adds a cup of water at standard power if the pump is already primed. If your controller was made after Nov 2011 you can turn down the pump inside the controller if your tank is small, this is covered in the manual. At the lowest speed it will only add a half cup. On an older controller, if needed you can add a Two Little Fishies Microvalve to the end of the hose to restrict the flow and reduce how much is added.