Abstract: A method and system are described for preventing flooding of a gas analyzer of the type wherein a pump conveys gas to be analyzed to a sample cell and a filter separates water from the gas flowing to the pump. The presence of excess liquid in the system is sensed by a pressure transducer which decouples the output of the pump from the sample cell and feeds it back to the filter. This results in an increase in pressure in the filter to prevent excess liquid from flooding the gas analyzer. The pressure is so held until the excess liquid passes from the filter system, after which the system returns to normal operation.