When it comes to pulling solid fish waste out of your aquaponics system, growers typically reach for one of three approaches: a swirl filter, a raft filter, or a clarifier. Technically, the swirl filter and the clarifier aren’t true filters — they’re settling devices, meaning solids drop to the bottom under gravity rather than being physically strained out. A raft filter, by contrast, actually filters solids out of the water. That doesn’t make the settling methods any less useful; they simply work on a different principle.

How does a clarifier in aquaponics work?

A clarifier is built around a diffuser or separator plate positioned in the middle of a tank. Round tanks are the most common shape, but square or rectangular tanks work fine too — unlike a swirl filter, a clarifier doesn’t rely on the water spinning, so tank shape isn’t critical.

Incoming water gets redirected toward the bottom of the tank, giving heavier solids room to sink while the cleared water rises past the separator plate and exits on the other side. Leave at least a one-foot gap at the bottom of the tank so settled solids have somewhere to accumulate. One popular way to pull water off the top of the fish tank and into the clarifier is an SLO (solids-lifting overflow). From there, the clarified water continues on to the rest of your setup — whether that’s a media bed, floating rafts, or another system component.

As solids accumulate in the bottom of the clarifier, you’ll need to drain them out periodically, either to a mineralization tank or straight onto your garden as fertilizer (plants respond well to it). The University of the Virgin Islands (UVI) system is a well-known real-world example of this design; their operation drains accumulated solids from the clarifier once per day.

Retention time in a clarifier

Whether you’re using a clarifier or any other settling tank, keeping the water velocity low is essential. Aim for a minimum retention time (also called detention time) of 20 minutes inside the clarifier. For example, a 50-gallon drum used as a clarifier could handle a maximum flow rate of about 150 gallons per hour and still hit that 20-minute target — since 20 minutes is a third of an hour, 50 gallons multiplied by 3 gives you 150 gallons per hour.

If your system’s flow rate makes hitting 20 minutes of retention time difficult, you have three main options:

• Add a second clarifier in parallel. Splitting the flow between two clarifiers effectively cuts the flow rate through each one in half. Two 50-gallon drums running in parallel, for instance, could together handle 300 gallons per hour.
• Upsize your clarifier. A larger tank holds more volume, which naturally extends the retention time for a given flow rate.
• Add a bypass. This option is a bit more involved, so it’s worth a closer look.

Using a bypass in a clarifier

A bypass works by diverting a portion of your flow around the clarifier. Say you have a single 50-gallon clarifier but a flow rate of 300 gallons per hour running through your system. Doing the math, that works out to just 10 minutes of retention time (60 minutes divided by 6), which isn’t nearly enough time for solids to settle out.

The fix is to siphon off part of that flow and send it directly to your grow beds, floating rafts, or wherever else in the system it needs to go — bypassing the clarifier entirely for that portion of the water. Since you want the bypassed water to be as clean as possible, you should draw it from just beneath the surface of the fish tank, which is typically where the cleanest water sits. In practice, this means installing an overflow fitted with a baffle, so you’re only pulling water from just under the surface rather than the surface itself. Both the top and bottom of the baffle should be covered with netting to keep fish from getting into the pipe. A ball valve on this line lets you dial in how much flow you divert — the more water you send through the bypass, the less flows through the clarifier, which stretches out the clarifier’s retention time.

Draining the solids

A clarifier with a conical bottom sloped at roughly 45 to 60 degrees drains solids most efficiently. If you’d rather not buy a purpose-built clarifier, you can build a serviceable one yourself — a 55-gallon drum is a common choice. The catch is that these drums have a flat bottom, which makes draining solids trickier since they don’t come with a built-in bottom valve.

To work around that, fit a pipe with a 90-degree elbow pointed down at the bottom of the drum. When you open the valve on that pipe, the weight of the water above pushes the settled solids out through the piping.

FAQ: Do you need a solids filter if you’re using a media bed?

If your grow bed includes worms, your system can tolerate some solids passing through, since the worms break the waste down and mineralize it in a way that benefits your plants. That said, running a separate mineralization tank for this purpose is generally the better approach. The more solid waste that reaches your media beds, the faster the media clogs and the more likely you are to develop low-oxygen zones in the system.

The bottom line: skipping solids filtration is possible, but if you do, plan on cleaning out your grow beds about once a year.