Few of us enjoy cleaning but there are times when cleaning is necessary to ensure and maintain good health of natural systems.  Aquaponics is no different in that the solids from the fish, roots from harvested plants and breakdown of the bacteria in the bed all contribute solid matter that does eventually limit the movement of water between/through the stones, and ultimately blocks areas of the bed to water flow.
 
In an ebb-and-flow aquaponics system we use growbeds to serve several simultaneous functions, these include a rooting substrate for the plants that provides mass as a counter balance, keeping the plants upright.  The stones trap solid matter coming from the fish tanks, aka faeces, providing the heterotrophic bacteria in the beds with a source of food.  Urine (in the loosest of terms) from the fish is rich in ammonia which is toxic, but the autotrophic bacteria living on the stones utilise this as their food source, converting the poisonous ammonia to nitrate.  Plants can utilise nitrate easily and they use this as their nitrogen source for growth.  In this process the solid and dissolved wastes produced by the fish are all dealt with by the growbeds, leaving the water clean to again return to the fish.
 
The intermittent filling and draining of the growbeds during normal operation allows water and nutrients to be supplied to the plants and bacteria at high tide, alternating with low tide during which air is sucked into the gaps between the stones as the water drains out of the bed.  Oxygen from the air is supplied in abundance to the bacteria and plant roots, ensuring these elements remain really healthy and able to perform their tasks efficiently.  Studies have shown that the microorganism colony within a healthy aquaponics growbed create an excellent environment for plant growth because these creatures suppress plant root pathogens.
 
Aquaponics is a natural system, and solid accumulation from the fish and bacteria will eventually clog up the gaps between the stones in the beds.  As this happens the gaps get increasingly smaller, trapping even finer particles and eventually blocking completely, causing the water to flow around that part of the bed.  This is a serious problem for several reasons, including that the oxygen is no longer supplied to the bacteria and plant roots as draining does not occur properly, exchanging the amazingly healthy environment we had for one where root pathogens can thrive.  Most plants struggle under these conditions and do not reach their commercial production targets.  Also, under these conditions anaerobic conditions prevail – in other words the normal bacteria are suppressed - and a new set of bacteria are encouraged to live in the beds.  These bacteria release hydrogen sulphide which is an extremely toxic substance.
 
A pre-filter can be in incorporated between the fish and the growbeds, but this does reduce the nutrient supply from the fish to the plants.  I prefer to supply the fish water directly to the plants and scale the two components so that the beds need cleaning only about once per year.  Cleaning a 2.5 x 1.2m growbed takes 2 people about an hour.  Obviously, there are no crops in the bed during cleaning!  We remove about ¼ of the stones from the water inlet end of the bed and place them in wheelbarrows next to the tank.  Then, starting at edge of the stone closest to the inlet, we wash the stones by turning them multiple times in the water, whilst siphoning the water to waste at the same rate at which new water enters the bed.  Progress slowly across the length of the bed moving the dirty stones into the water and siphoning out the dirty water continuously.  Finally, the stones in the wheelbarrows are also rinsed before being returned to the beds.  Do not worry about losing the bacteria during this process as they are extremely hardy and re-establish their population again rapidly following this washing.
  
Few of us enjoy cleaning growbeds but it is vital in order to maintain healthy plants and bacteria, and for the magic of aquaponics to continue.