A method of operating an inkjet printer identifies a thermal load that will be imposed on the printheads in the inkjet printer during execution of a print job and identifies a remedial action to reduce the thermal load if the thermal load increases the temperature of the printheads above an upper threshold of a predetermined temperature range. The thermal load is identified from the ink image content data for the print job, the print job parameters for the print job, and environmental condition measurements received from sensors in the printer. The remedial actions include manipulation of the print job queue, alteration of print job parameters, and active cooling to remove heat from the printheads or media within the printer.