These cationic, surface active chemicals are organically substituted nitrogen compounds. The general structure of these microbiocides is shown below:

"R" represents alkyl, aryl or heterocyclic radical substitutes containing 8 to 25 carbon atoms bound to a nitrogen atom. The total cationic portion is associated with a halide ion.

Quaternaries are generally most effective against algae and bacteria in alkaline pH ranges. Their microstatic action is attributed to their cationic charge, which forms an electrostatic bond with the negatively charged sites on the cell wall. The electrostatic bonds create stresses in the cell wall, causing cell lysis and death. The quaternaries also cause cell death through protein denaturation, by distorting the permeability of the cell wall and reducing the normal flow of life-sustaining nutrients into the cell.

A number of problems limit the use of these compounds. Their activity level drops in systems heavily fouled with dirt, oil and debris.

Because of their surface activity, "quats" will emulsify oil, instead of participating in cell wall bonding — a competing mechanism which weakens the control program. In addition, overfeed of "quats" may cause extensive foam.