Desalination plants have an important concern regarding controlling the permeate flow rate and pH during operability. This paper proposes the proportional integral derivative (PID) control design using modified Particle Swarm Optimization (PSO) techniques called autonomous groups PSO (AGPSO) in the two-input two-output (TITO) RO desalination plant to control the permeate flow rate and pH. Here, three different versions (AGPSO1, AGPSO2, and AGPSO3) of the AGPSO algorithm are utilized to design PID control for the same TITO plant. In addition, an integral time absolute error (JITAE) based objective function is utilized to design a PID controller. The simulation results suggest that the proposed controller designs are flexible, self-tuning, and have stable characteristics, while the AGPSO3-PID control design attained a robust design for optimum tuning compared to existing improved grey wolf optimization PID (IGWO-PID) and other versions of AGPSO based PIDs (AGPSO1-PID, AGPSO2-PID). The design of AGPSO-PID achieved a minimum objective function than existing IGWO-PID and other versions of AGPSO based PIDs {AGPSO1-PID, AGPSO2-PID}. Finally, the proposed controller designs outperform the existing IGWO-PID design in literature in terms of control performance, demonstrating a precise control for and the improvement of plant performance.