The rescue unfolded after marine pilots first spotted the pod a day earlier, noting the whales were disoriented and drifting in opposite directions.
Lyn Kindlen, harbour master, explained that the crew had to pause repeatedly, assessing each whale's condition before adjusting the plan.
The operation, which spanned six hours, involved eight boats and coordinated efforts from British Divers Marine Life Rescue, local authorities in Gravesham and Thurrock, and the Port of London Authority.
While most of the pod returned safely, a mother and her calf required extra rest, extending the mission.
Two whales later died: one washed up unwell, another surfaced after a return attempt but was found dead on shore.
The authorities will now monitor the released whales' return to deeper waters, and the incident has prompted discussions on river safety.