This work develops a simple and non-distributed control of a specific structure of electrochemical tubular reactor system, which is used to remove the hexavalent chromium Cr(VI) from wastewaters. Through the composite finite difference combination, the coupled nonlinear partial differential equations (PDEs) under Danckwerts boundary conditions can be numerically solved by the Matlab PDE solver. The multi-loop PID control scheme is successfully implemented to the output regulation of the wastewater treatment process.