After an initial investigation, further allegations emerged in April, leading British Canoeing to approach UK Sport to help commission a second probe.
That was completed and a disciplinary hearing had begun, but it has now been abandoned.
British Canoeing said the resignation of the performance team coach "brings the disciplinary process to an end".
The British team enjoyed its most successful Olympic Games in Rio last year, with competitors winning two gold medals and two silvers.
ParalympicsGB then claimed three gold and two bronze medals at the Rio Paralympics, where they topped the medal table.
April's revelations came amid mounting concern over the culture of high-performance programmes at British sports, and whether medal success has come at the expense of athlete welfare.
And on Thursday, British Olympic bobsleigh athlete Rebekah Wilson told BBC Sport she would secretly cut and try to concuss herself as the "intense pressure" of training took its toll.
Earlier this year, BBC Sport revealed British Swimming is conducting an investigation after bullying complaints were made by a number of Paralympians about a coach.
And British Cycling apologised for various "failings" after an independent review into allegations of bullying and sexism.
A British Canoeing coach who has been suspended since December amid abuse allegations has resigned.