The Makara I think is not based on one single animal but seems more like a composite of different ones. Usually I've seen different versions of this creature and many have composite features of animals like dolphin, shark, crocodile, elephant, and deer. Its fluidity is apparent when I saw the Chinese version of it, which is heavily dragonified.
As far as the reason of this creature, maybe it has something to do with each Hindu deity having their own magical animal mount (the bird god Garuda for Vishnu, the elephant Airavata for Indra, etc). Since the Makara is the only major mount for the water god Varuna and the river goddess Ganga, maybe it's an inventive tie to the typical large beasts of the land associated with the water.
I don't think the elephant seal was the source for the Makara.
the word makara is the original term given to the mugger crocodile, and thus the makara of indian art was represented as a vahana of kamadeva and also i think ganga, as a crocodilian beast. later, it was given both fishlike and turtle-like features alternatively, sometimes as a chimera of all three. when the makara motif reached sri lanka, it was interpreted as a complete chimera, mainly with an elephant's trunk, fish scales, the ears of a pig, eyes of a monkey, teeth and jaws of a crocodile, wings of a bird ( in more modern depictions) and i think the paws of a lion. but these features are certainly not consistent and different artists interpret them differently.