The department shall allow an appropriate schedule of compliance for a permittee to make upgrades or changes to its facilities that are necessary to meet new water quality requirements. For publicly owned treatment works, schedules of compliance shall be consistent with affordability findings made under section 644.145. For privately owned treatment works, schedules of compliance shall be negotiated with the facilities recognizing their financial capabilities and shall reflect statewide performance expectations. The department shall incorporate new water quality requirements into existing permits at the time of permit renewal unless there are compelling reasons to implement these requirements earlier through permit modifications. All new permit applicants may be required to meet any new water quality standards or classifications prescribed by the commission.