Hydroton is usually full of fine clay hydroton dust when it is delivered in the bags. If you did not thoroughly rinse it, stirring it continuously with a stick or similar to make sure all the dust runs away, (this can take some time until the water runs clear), you will end up with cloudy water in your aquaponics system. Hydroton dust is also quite acid, since it is clay, and will affect the pH of your water.
This hydroton dust will also accumulate in your pipes and tubing and could clog valves and outlets. So to get rid of hydroton dust, you will need to install temporary additional mechanical filtration. This means an additonal box filter such as the one pictured, left.
When I had this problem, what I did was acquire some heavy duty aquarium box filters in a job lot on EBay. This cost me around £10 for the lot. They have an inside cylindrical sponge filter which can easily be rinsed out under the tap.
I installed them in my fish tank, in the aquaponics system, which was yellow with dust and full of disturbed fish, plugged them in and switched them all on, and left them for an hour. By then the aquaponics system water was considerably clearer, but the flow rate through these filters had stopped, due to clogging with the hydroton dust.
So I unplugged them, hauled them out of the aquaponics system and to the sink, disassembled them and rinsed out the filter sponges under the tap, then reassembled them.
I reinstalled them in the tank and repeated the process until the aquaponics system water ran clear and there was no longer any hydroton dust clogging apparent in the filters. I then removed them.
Throughout this process, the water in the aquaponics system was being recirculated as normal, and afterwards the hydroton dust was no longer a problem.
It is worth keeping a box filter or to hand for water quality emergencies in your aquaponics system, since they do occur from time to time for various reasons, not just hydroton dust.
I recommend the aquaponics specialist books below to understand the ins and outs of successful aquaponics system management, whether on a small scale or in a large commercial enterprise. Cheaper than many of the short aquaponics how-to courses on offer!