This paper presents a novel technique to mitigate fouling and reduce effects of concentration polarization in reverse osmosis (RO) membranes. The technique will be referred to as the temporary step-wise cyclic operation. The method is based on superimposing a cyclic square pressure pulses on the operating pressure for a short period of time. The objective of this is to create a disturbance that may result in cleaning the membrane from reversible foulants and, hence, restoring the membrane to its normal operation. The periodic square pressure pulses were generated by superimposing oscil-latory pressure pulses on the operating pressure to create instabilities. Although the use of fluid instabilities is not a new subject, the work presented here attempts to demonstrate how to program an industrial distributed control system (DCS) to perform periodic operation. The technique was implemented on a laboratory-scale RO unit that was interfaced to a Yokogawa Centum VP DCS. After the initial verification runs, the periodic operation using square wave functions of RO process was automatically performed by a DCS program, which was programmed to generate a pseudorandom binary signal course with varied frequencies superimposed on a linear control signal, thus resulting a square wave pressure signal which was onset for a short period generating eddies and turbulence that were instrumental in mitigating fouling and reduce concentration polarization. A 28.7% improvement in the permeation rate was achieved by comparing the permeate flow rate before and after imposing the mitigation technique using the superimposed square wave pressure pulse. On top of that, a reduction of conductivity from 920 to 287 µs/cm was also achieved. A comparative study on a second membrane also shows an increase of about 16% on flow rate and the conductivity came down from 1,021 to 477 µs/cm. © 2019 Desalination Publications. All rights reserved.