Secondary treatment is the second step in the treatment train.   This step further separates solids so that after secondary treatment, at least 85% of the total suspended solids (TSS; organic or inorganic particles either suspended in or carried by water) and at least 85% of the biological oxygen demand (BODs; the demand for oxygen produced by solids suspended in water necessary for the substances to break down) are removed.  Microorganisms are stimulated by bubbling oxygen into wastewater to break down organic matter in a process called "activated sludge treatment."   This treatment is followed by a settling period to separate solids (including the microorganisms for this process) from the wastewater.

Secondary treatment also removes certain amounts of other pollutants, such as metals and contaminants, because they have a tendency to bind or attach to solids removed during this step.

In New Jersey, all ocean wastewater dischargers receive treated wastewater from secondary treatment plants.