Around 30 to 40% of the food provided to cultured fish is turned into solid waste (i.e., feces and uneaten food). To maintain an appropriate environment, solid wastes must be removed from the culture water before they have a chance to degrade and use up oxygen.

In a recirculating system, water typically flows from the fish tank by gravity into a vessel that removes solid wastes. The most common technique to remove the larger, heavier "settleable solids" is a simple settling basin. This is typically an unstocked tank where a small volume of water flowing from the culture tank is slowed by a larger volume of water, causing heavier particles (solid waste) to settle out. In settling basins, about 6-10 minutes of detention time is necessary.

An effective type of settling basin is the "swirl or cyclone" separator which has a cone shaped floor to concentrate the waste for removal. Another improvement to the simple settling basin is the addition of a weir, sheets of polyester matting or use of a plastic media that serves to slow the flow of water and settle more solids out. Tube or "inclined plane" clarifiers, usually using "bio deck" (see section on biofilters, below), are well suited for classroom systems (i.e., low tech, can be hand made, take up less space and reduce water retention time by half). Commercial producers sometimes use mechanical filtration, with screens of 100 to 140 micron holes, to remove larger solids.

Some systems employ the use of a secondary clarifier to remove smaller particles known as suspended and/or dissolved solids. Techniques to remove suspended solids include the use of sand filters and plastic bead filters. These filters trap particles and the "media" (e.g., sand, beads) is fluidized periodically to remove the waste particles in a settling cone.

The most common technique for removal of dissolved solids is the use of a foam fractionator. In a foam fractionater, the "dirty" water flows down a pipe while air bubbles rise up the pipe rapidly. The dissolved solids attach themselves to the rising bubbles and come out the top of the pipe as a brown foam.