Methods and systems are provided for controlling an automatic separator apparatus of a Materials Recovery Facility. A separator for separating a stream of recyclable paper and containers into a paper stream including primarily paper and a container stream including primarily containers is provided. The separator has at least one adjustable operating parameter. A first detector detects an amount of container contaminants in the paper stream. A second detector detects an amount of paper contaminants in the container stream. A control system operably connected to the separator and the first and second detectors adjust the adjustable operating parameter so as to reduce a combined measure of contaminants in the paper stream and in the container stream.