An inkjet printer adjusts operation of a vacuum system coupled to a printhead to compensate for pressure changes in the manifold of the printhead caused by vertical displacement of the printhead within the printer. The inkjet printer includes a controller that determines either a difference between an optimal pressure in the manifold and a current pressure to operate a vacuum coupled to the manifold for pressure adjustment or it correlates a current printhead vertical position to a previously observed vertical position and uses a vacuum value associated with the previously observed vertical position to operate the vacuum.