In this paper, we propose an operation procedure for our previously developed in-pipe robotic system that is used for water quality monitoring in water distribution systems (WDS). The proposed operation procedure synchronizes a developed wireless communication system that is suitable for harsh environments of soil, water, and rock with a multi-phase control algorithm. The new wireless control algorithm facilitates smart navigation and near real-time wireless data transmission during operation for our in-pipe robot in WDS. The smart navigation enables the robot to pass through different configurations of the pipeline with long inspection capability with a battery in which is mounted on the robot. To this end, we have divided the operation procedure into five steps that assign a specific motion control phase and wireless communication task to the robot. We describe each step and the algorithm associated with that step in this paper. The proposed robotic system defines the configuration type in each pipeline with the pre-programmed pipeline map that is given to the robot before the operation and the wireless communication system. The wireless communication system includes some relay nodes that perform bi-directional communication in the operation procedure. The developed wireless robotic system along with operation procedure facilitates localization and navigation for the robot toward long-distance inspection in WDS.