An improved method for operating a tunnel type pasteurization system has each temperature zone with a separate sump (16) to collect heat treatment water and with a separate pump (20) to run water over the products as they pass through each zone, and/or to pump water to other zones. The sumps are sufficiently large to take excess water and are fitted with level monitors and temperature sensors. The water is heated/cooled via heat exchangers. The versatile control system is especially useful for startup and for rapid process changes.
