The team won two golds and two silvers at the Rio Olympics, plus three golds and two bronzes in the Paralympics, but it has joined other successful British sports including swimming and cycling in being hit by a variety of allegations such as sexual abuse, racism, sexism or bullying by coaches.
The sport's governing body did not name the coach who resigned but said the individual was suspended in December, pending its investigation.
The Guardian newspaper reported in June that several athletes had reported sexual misconduct by the coach.
"The investigation was completed and a disciplinary hearing commenced but was adjourned," British Canoeing said on its website.
"The resignation of the individual brings the disciplinary process to an end and British Canoeing will be unable to provide further comment."
(Reporting by Steve Tongue; Editing by Robin Pomeroy)
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