The retailer said its outlets at Dawson Street and Jervis Street would shut on Sunday.
The shops employ 46 people between them.
Hodges Figgis, one of the capital’s best known bookshops, which is owned by Waterstones, will not be affected, the company said.
A Waterstones spokesman said that there may be some opportunities to move staff to other outlets but that there would be redundancies.
Other branches in Cork, Drogheda, Ballymena, Belfast, Coleraine and Newry will not be hit by the Ireland and British-wide round of closures.
Waterstones also said that there were no plans to rebrand the Hodges Figgis store.
Last month HMV Group — Waterstones parent company — said that it was forced into a raft of cost-cutting measures as it battled with tumbling sales.