An HVAC control system for directing the flow of air in a work vehicle's HVAC system responds to the orientation of a rotating seat within the work vehicle's cabin. The seat may rotate between at least two operational positions, such that the operator of the work vehicle may control a forward or a rearward implement. The HVAC control system includes one or more detectors for detecting the position of the seat. A control module receives output from the detectors and allows or prevents the flow of air through particular ducts in the HVAC system based on the seat's position. The control module may actuate one or more doors to open and close ducts as needed. The control module may operate a first door to open or close forward ducts and a second door to open or close rearward ducts depending on whether the seat is facing forward or rearward.