An automated sample collection workstation is provided. The workstation includes a processor, a peristaltic pump, a valve actuator, and an algorithm. The peristaltic pump and the valve actuator are in electrical communication with the processor. The valve actuator can move a plurality of valves, when disposed therein, among an off position, a flush position, and a sample position. The algorithm is resident on the processor and is configured to: move all of the valves to the off position and place the pump in an off state when no sampling or flushing is required, move all of the valves to the flush position and place the pump in an on state for a predetermined flush time period when flushing is required, and move a respective one of the valves to the sample position, move any of the valves upstream of the respective valve to the flush position, and place the pump to the on state for a predetermined sample time period when a sample is required.