He will stand down on September 4.
Board chair Sir John Hansen informed staff this afternoon in an email, which said the move followed the opening of the West Coast's Te Nīkau Grey Hospital.
It will coincide with a planned move into the new Christchurch Hospital Hagley facility later this year.
In a statement, Meates said his time with the health boards had been "so incredibly rewarding".
"DHBs are some of the largest and most complex businesses in New Zealand and I have been really fortunate to work with some of the most gifted and talented teams, both in Canterbury and on the West Coast," he said.
"The care provided by clinical and support teams, both in our hospitals and in primary and community care, has been exemplary in spite of them working in environments that in many cases have been and remain challenging."
Sir John said Meates led Canterbury's health system through some of the biggest and most challenging events New Zealand has ever faced, including the Christchurch and Kaikōura earthquakes and the mosque attacks.
"David's leadership during and following these extraordinary events was exemplary," he said.
He said Meates' legacy included modern state-of-the-art health facilities at Te Nīkau in Greymouth, the Kaikōura Health Centre, Burwood Hospital, Christchurch Hospital Hagley, Akaroa, Rangiora, Ashburton, state of the art digital platforms and analytics, and the Health Precinct.
In a statement, Health Minister Chris Hipkins said he wanted to thank Meates for his many years of dedicated service to the people of Canterbury and the West Coast.
"Being the chief executive of a District Health Board is no easy job at the best of times. David has provided strong leadership - particularly in the wake of the Canterbury earthquakes. I wish him well for his future endeavours," he said.
Both health boards are under significant pressure to reduce their deficit.
Resignation a 'disaster' for public health
The union of senior doctors, Association of Salaried Medical Specialists, says Meates' resignation is a 'disaster' for public health, with executive director Sarah Dalton saying the board forced him out.
She said senior clinicians backed him.
"I feel that they were very strongly in support of what was going on there, I think it's a disaster for Canterbury, there seems to be a hostile board down there, I think they put balance sheets ahead of the well-being of people."
She said putting numbers ahead of the people is not a responsible governance strategy for DHB.
"The Board has repeatedly failed to listen to the advice of its senior management and clinical leaders and in my view has acted unethically. The chair should have the courage to stand up to the Government and speak up for Cantabrians instead of asking DHB management to force cuts to healthcare and facilities that will ultimately leave the health system unfit for purpose - and potentially unsafe", she said in a statement.
"The sorry result of this Board's failings is the loss of an effective DHB chief executive and a number of his team at a time when the health system can ill-afford to lose strong, experienced leadership," Dalton said.
