In a process and apparatus for treating produced water, the produced water flows through a series of treatment units. A portion of the produced water may by-pass one or more of the treatment units but the by-pass portion may be such that the treated water is still acceptable, for example for discharge or reuse. Concentrations of oil and grease, organic carbon, silica, pH or related parameters in the produced water may be monitored and used to control the process or apparatus. Control of the process may involve one or more of altering a by-pass portion, altering the addition of chemicals, and altering the operation of a unit process. The process may be controlled to respond to upset conditions, or such that the concentration of one or more limiting contaminants is near, but not over, a specified maximum for re-use or discharge.