The behavioural transition from filial dependence to weaning in harbour seal pups is poorly understood. Here we trace progressive changes in pup behaviour with the mother at two pupping sites in Dundrum Bay, north-east Ireland, and describe the behaviour of ‘lone pups’ in their mothers’ absence. We found that pups engaged in progressively fewer nosing contacts with their mother, but mother-pup body contact and suckling frequency did not decline, and mothers did not reject their pup’s nursing solicitations. From around two weeks of age ‘lone’ pups were observed while unattended by their mother. Lone pups approached the haul-out site singly, in dyads or threesomes, interacted with one another in the water, and tended to rest onshore beside one another. Mothers and lone pups often reunited at a specific area within one of the sites. Pups of an estimated 3.5-7 weeks of age were often seen giving a wide open-mouth gape shortly after hauling out, suggestive of preliminary digestion of fish. We discuss these behaviours of pups in Dundrum Bay in the context of other harbour seal populations and conclude that behaviour at weaning is flexible within the species, allowing behaviour to adapt to local habitat conditions and prey availability.