Pinnipeds have great potential for comparative studies of mother—pup recognition due to the contrasting maternal strategies adopted by otariids and phocids. Typically, otariid mothers perform foraging trips during lactation, leaving their pups in the colony, whereas phocid mothers remain close by their pups during the entire nursing period. Unlike most phocids, harbor seal (Phoca vitulina) females forage during the nursing period, which exacerbates the need for effective mother—pup vocal recognition in this species. Individual differences and ontogeny-related changes in airborne and underwater harbor seal mother attraction calls were investigated. Acoustic differences between aerial and underwater components of amphibious pup calls were also assessed. Sixteen acoustic parameters were measured on 1,072 calls from 88 pups recorded during the 2011–2013 breeding seasons in the St. Lawrence Estuary, Canada. Discriminant function analysis (DFA) correctly assigned 42.6% and 44.2% of airborne and underwater calls, respectively, to individual pups. A majority of highly individualized acoustic parameters were affected by pup age and body length. These results indicated that harbor seal pup calls encode an individual signature that might allow recognition of young by mothers, in which case females must continuously learn their pup's changing voice throughout of the rearing period. The fundamental frequency, total duration, and frequency-modulation slopes were constant between aerial and underwater components of amphibious calls. This could facilitate females' memorization of these highly individualized acoustic parameters to identify their offspring's call in both media.