Backyard Aquaponics
A place to discuss aquaponics

Will the bacteria do their job better when soaked in still water? or in flowing water? Or a combination of both as per my example below?

Consider this, an IBC on timed Flood and Drain (stand pipe set-up, no siphons) 15 on 45 off. CHIFT PIST.

1000L FT turning over the full volume every 15 minutes (therefore pumping at 4000 L/h). Filtering with say a 1000L grow bed that's 60% gravel, 40% water. So the GB fills with water in the first 6 minutes of the Flooding cycle. Making for the next 9 minutes a total of 600L overflowing down the stand pipe and returning to the sump. Then finally draining via the small hole in the base of the stand pipe once the pump turns off.

How efficient are the bacteria at cleaning the water when it is flowing over the rocks as opposed to when it just being soaked for 15 minutes?

All to do with DO. The bacteria in an AP system are predominantly aerobic and they don't mind being submerged, and will continue working, for as long as there is DO to sustain them. It's the same for the plants in a raft the system too, they will grow in water (which would normally drown them) provided the DO is kept high. Actually think of the bacteria as a person with scuba gear - the person can keep working under water until the air in the tank runs out, or until she exchanges her tank. The DO is like tank air to plants and aerobic bacteria and must be replenished at regular intervals.

Another factor is load and carrying capacity. The higher the raw nutrient load, the greater the numbers of bacteria required to consume same, the faster the bacteria consume the oxygen. All things being equal, which they never are, the faster the flowing water over/through the media the greater the DO, the better the aerobic bacteria can work due to the greater potential numbers of bacteria that can be supported - up to a point. At some point it stops being a grow bed and resembles a mineralization device where plants won't survive. In the end it's all about balance.

The rule of thumb though for a 1:1 or 1:2 system is 15 on, 45 off, and that seems to work well by all accounts.

The nitrifying bacteria actually "live" in the trillions of small holes in media like hydroton and within a thin film of surface water bound by surface tension.... effectively, they're always immersed...

As McFarm says... it's all about the DO content of the water...

The bacteria don't like to get dry, but they don't want to go without O2 either. Stagnant water makes for anaerobic activity, flowing water tends to be more aerobic. I have run fishtanks with undergravel filters for years, and they scrub the water well, but they do a better job with more water flow, and with more DO.