Hi There, Aquaponics has been used in the past in conjunction with AutoPot, we used to have an acre nursery in Bangkok, they used a very technical filtration system to avoid particle issues. If you are a home grower I would suggest you use the Pro Filter, flush the pipe more regularly and clean the filter out more frequently and you should be fine …… the new AQUAvalve 5 has a much larger inlet now and very much reduces potential blockages.