Ottakar's shops will be rebranded to HMV's Waterston's fascia, supplier terms will be harmonised and Waterstone's stock management system will be installed.
Three Ottakar's offices - in Salisbury, Clapham and London Bridge - will be shut with the loss of approximately 100 jobs.
Waterstone's managing director Gerry Johnson will lead the melding of the businesses, but it was confirmed that Ottakar's chief executive James Heneage and finance director Michael Hitchcock will 'remain on a consultancy basis for a limited period to assist with the transition.'
Johnson said: 'This is a very thorough programme for combining the best aspects of the Waterstone's and Ottakar's businesses in the shortest amount of time which is sensible.
'I am confident that with the addition of the fantastic bookselling skills of our new colleagues at Ottakar's, we will continue to offer customers the best book-buying experience on the high street.'
A combined operations management structure will be introduced and regional managers from both booksellers appointed.
HMV completed the£63 million acquisition of Ottakar's on Monday, after a lengthy competition inquiry and in the face of opposition from well-known authors and some publishers. The retailer expects the deal to deliver synergies of£10 million in 2007/08 and believes its greater scale will enable Waterstone's to cope with the growing competitive threat from grocers and e-tailers.